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DQo8L2Rpdj4NCjwvYmxvY2txdW90ZT4NCjwvZGl2Pg0KPC9ib2R5Pg0KPC9odG1sPg0K --_000_143F40A59C364F0F92556ED6220149D5kofompgde_-- From owner-chemistry@ccl.net Thu Jun 10 11:49:00 2021 From: "Andrew Pudzianowski bluesquantum-,-gmail.com" To: CCL Subject: CCL: QM codes NOT written in Fortran Message-Id: <-54377-210610004342-29143-Ysv47WrohPHMPL/DABJRsg[#]server.ccl.net> X-Original-From: Andrew Pudzianowski Content-Type: multipart/alternative; boundary="000000000000cdd5ae05c46208d6" Date: Thu, 10 Jun 2021 00:43:25 -0400 MIME-Version: 1.0 Sent to CCL by: Andrew Pudzianowski [bluesquantum _ gmail.com] --000000000000cdd5ae05c46208d6 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable ORCA, from the group of Frank Neese, is written in C++. Cheers....Andrew Pudzianowski On Wed, Jun 9, 2021 at 9:51 PM Joe Leonard jleonard42%x%gmail.com < owner-chemistry _ ccl.net> wrote: > Folks, are there QM packages that have managed to =E2=80=9Close=E2=80=9D = all their fortran > code or are new enough to have been developed in a different language or > different languages? I have not seen good comments re: the Mac M1 chipse= t > and I=E2=80=99m curious whether there are alternatives=E2=80=A6 > > I=E2=80=99m sure others would be interested as well. > > Joe Leonard > =E2=80=94 > "Peter Thiel was right, we just can't build cool sh*t anymore. I really > did want a flying car, and all I have is 140 characters and promises of A= I > that never come true." > > --000000000000cdd5ae05c46208d6 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
ORCA, from the group of Frank Neese, is written in C++. Ch= eers....Andrew Pudzianowski

On Wed, Jun 9, 2021 at 9:51 PM Joe Leonard j= leonard42%x%gmail.com <owner-chemistry _ ccl.net> wrote:
=
Folks, are there QM packages that have managed to =E2=80= =9Close=E2=80=9D all their fortran code or are new enough to have been deve= loped in a different language or different languages?=C2=A0 I have not seen= good comments re: the Mac M1 chipset and I=E2=80=99m curious whether there= are alternatives=E2=80=A6

I=E2=80=99m sure others would= be interested as well.

Joe Leonard
<= div style=3D"text-align:start;text-indent:0px">
<= div style=3D"text-align:start;text-indent:0px">
=E2=80=94
"Peter Thiel was right, we just = can't build=C2=A0cool sh*t anymore. I really did want a=C2=A0flying car= , and all I have is 140=C2=A0characters and promises of AI that never=C2=A0= come true."
<= /div>
<= /div>
<= /div>
<= /div>
<= /div>
<= /div>

--000000000000cdd5ae05c46208d6-- From owner-chemistry@ccl.net Thu Jun 10 12:24:01 2021 From: "Phil Hasnip phil.hasnip~~york.ac.uk" To: CCL Subject: CCL: QM codes NOT written in Fortran Message-Id: <-54378-210610050846-25203-Ij7vAUrOGkHPmAxn/4C4yw^_^server.ccl.net> X-Original-From: Phil Hasnip Content-Type: multipart/alternative; boundary="0000000000009e20ae05c465bc94" Date: Thu, 10 Jun 2021 10:08:27 +0100 MIME-Version: 1.0 Sent to CCL by: Phil Hasnip [phil.hasnip^_^york.ac.uk] --0000000000009e20ae05c465bc94 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable Dear J=C3=BCrgen, Thank you, I intended to write Python/C but clearly my brain did not communicate that to my fingers! I appreciate you correcting me. Not that you can't write a QM program entirely in Python, but the performance would be too poor to use in any research context. All the best, Phil ---------------------------------------------------------------------------= --------- Dr Phil Hasnip Email: phil.hasnip(_)york.ac.uk EPSRC RSE Fellow Web: www-users.york.ac.uk/~pjh503 Dept of Physics University of York Tel: +44 (0)1904 322225 York YO10 5DD On Thu, 10 Jun 2021 at 09:47, J=C3=BCrgen Gr=C3=A4fenstein jurgen.grafenste= in#%# chem.gu.se wrote: > Dear Phil, > > GPAW is actually written in a combination of C (for the hard-core part) > and Python (for the high-level layer). You can find more information here= : > > https://www.sciencedirect.com/science/article/pii/S1877050911000615 > > Best regards, > J=C3=BCrgen > > _____________________________________ > J=C3=BCrgen Gr=C3=A4fenstein > University of Gothenburg > Dept of Chemistry and Molecular Biology > SE-412 96 G=C3=B6teborg > Sweden > > jurgen.grafenstein(_)chem.gu.se > > On 10 Jun 2021, at 04:07, Phil Hasnip phil.hasnip[-]york.ac.uk < > owner-chemistry(_)ccl.net> wrote: > > Dear Joe, > > Yes there are, for example GPAW is written in Python. However, the choice > of many QM programs to use Fortran is not simply because they are "old" > codes, many newer QM packages have deliberately chosen Fortran over > alternatives (e.g. C++). QM simulations are computationally intensive, an= d > Fortran is rather hard to beat performance-wise -- though modern C++ > compilers are competitive these days (albeit with compiler development > teams an order of magnitude larger than the corresponding Fortran ones). > Fortran also has many modern features which are still lacking in most > mainstream languages, for example partitioned global-address space > (coarrays). > > I don't see much incentive to move the millions of lines of Fortran into > another language, but what is becoming increasingly common is to develop = a > high-level software layer in something else, usually Python, which allows > more rapid prototyping and development, whilst keeping all the > numerically-intensive work in Fortran or C++. > > I'm confused about your Mac M1 chipset reference; how does this relate to > your Fortran question? There are good ARM Fortran compilers, if that's wh= at > you're worried about. > > All the best, > > Phil Hasnip > > > -------------------------------------------------------------------------= ----------- > Dr Phil Hasnip Email: phil.hasnip**york.ac.uk > EPSRC RSE Fellow Web: www-users.york.ac.uk/~pjh503 > Dept of Physics > University of York Tel: +44 (0)1904 322225 > York YO10 5DD > > > On Thu, 10 Jun 2021 at 01:58, Joe Leonard jleonard42%x%gmail.com < > owner-chemistry**ccl.net> wrote: > >> Folks, are there QM packages that have managed to =E2=80=9Close=E2=80=9D= all their >> fortran code or are new enough to have been developed in a different >> language or different languages? I have not seen good comments re: the = Mac >> M1 chipset and I=E2=80=99m curious whether there are alternatives=E2=80= =A6 >> >> I=E2=80=99m sure others would be interested as well. >> >> Joe Leonard >> =E2=80=94 >> "Peter Thiel was right, we just can't build cool sh*t anymore. I really >> did want a flying car, and all I have is 140 characters and promises of = AI >> that never come true." >> >> > --0000000000009e20ae05c465bc94 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Dear=C2=A0J=C3=BCrgen,

Thank you, I int= ended to write Python/C but clearly my brain did not communicate that to my= fingers! I appreciate you correcting me. Not that you can't write a QM= program entirely in Python, but the performance would be too poor to use i= n any research context.

All the best,
Phil

------------------------------------------------------------------------= ------------
Dr Phil Hasnip =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0=C2= =A0=C2=A0=C2=A0=C2=A0=C2=A0 Email: phil.hasnip(_)york.ac.uk
EPSRC RSE Fellow=C2=A0=C2= =A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 Web:=C2=A0 www-users.york.ac.uk/~pjh503<= br>Dept of Physics
University of York =C2=A0 =C2=A0 =C2=A0 =C2=A0=C2=A0= =C2=A0=C2=A0=C2=A0 Tel: =C2=A0=C2=A0=C2=A0 +44 (0)1904 322225
York YO10 = 5DD


On Thu, 10 Jun 2021 at 09:47, J=C3= =BCrgen Gr=C3=A4fenstein jurgen.grafenstein#%#chem.gu.se <owner-chemis= try(_)ccl.net> wrote:
Dear Phil,

GPAW is actually written in a combination of C (for the hard-core part= ) and Python (for the high-level layer). You can find more information here= :


Best regards,
J=C3=BCrgen

_____________________________________
J=C3=BCrgen Gr=C3=A4fenstein
University of Gothenburg
Dept of Chemistry and Molecular Biology
SE-412 96 G=C3=B6teborg
Sweden

jurgen= .grafenstein(_)chem.gu.se

On 10 Jun 2021, at 04:07, Phil Hasnip phil.hasnip[-]york.ac.uk <owner-chemistry(_)ccl.net> wrote:
Dear Joe,

Yes there are, for example GPAW is written in Python. However, the cho= ice of many QM programs to use Fortran is not simply because they=C2=A0are = "old" codes, many newer QM packages have deliberately chosen Fort= ran over alternatives (e.g. C++). QM simulations are computationally intensive, and Fortran is rather hard to beat performa= nce-wise -- though modern C++ compilers are competitive these days (albeit = with compiler development teams an order of magnitude larger than the corre= sponding Fortran ones). Fortran also has many modern features which are still lacking in most mainstream l= anguages, for example partitioned global-address space (coarrays).=C2=A0

I don't see much incentive to move the millions of lines of Fortra= n into another language, but what is becoming increasingly common is to dev= elop a high-level software layer in something else, usually Python, which a= llows more rapid prototyping and development, whilst keeping all the numerically-intensive work in Fort= ran or C++.

I'm confused about your Mac M1 chipset reference; how does this relate = to your Fortran question? There are good ARM Fortran compilers, if that'= ;s what you're worried about.=C2=A0

All the best,

Phil Hasnip

----------------------------------------------------------------------= --------------
Dr Phil Hasnip =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0=C2=A0=C2=A0=C2=A0= =C2=A0=C2=A0 Email: phil.hasnip**york.ac.uk
EPSRC RSE Fellow=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 Web:=C2=A0= www-users.york.ac.uk/~pjh503
Dept of Physics
University of York =C2=A0 =C2=A0 =C2=A0 =C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 Tel:= =C2=A0=C2=A0=C2=A0 +44 (0)1904 322225
York YO10 5DD


On Thu, 10 Jun 2021 at 01:58, Joe Leo= nard jleonard42%x%gmail.com= <owne= r-chemistry**ccl.net> wrote:
Folks, are there QM packages that have managed to =E2=80=9Close=E2=80= =9D all their fortran code or are new enough to have been developed in a di= fferent language or different languages?=C2=A0 I have not seen good comment= s re: the Mac M1 chipset and I=E2=80=99m curious whether there are alternatives=E2= =80=A6

I=E2=80=99m sure others would be interested as well.

Joe Leonard
=E2=80=94
"Peter Thiel was right= , we just can't build=C2=A0cool sh*t anymore. I really did want a=C2=A0= flying car, and all I have is 140=C2=A0characters and promises of AI that n= ever=C2=A0come true."


--0000000000009e20ae05c465bc94-- From owner-chemistry@ccl.net Thu Jun 10 12:59:00 2021 From: "Anatoli Korkin korkin. . .nanoandgiga.com" To: CCL Subject: CCL: MM/MD program for Windows PC Message-Id: <-54379-210610110720-3692-4QDIMzy0U5mzk0ei7W94hQ . server.ccl.net> X-Original-From: Anatoli Korkin Content-Type: multipart/alternative; boundary="000000000000d0c5fb05c46abee7" Date: Thu, 10 Jun 2021 10:06:59 -0500 MIME-Version: 1.0 Sent to CCL by: Anatoli Korkin [korkin a nanoandgiga.com] --000000000000d0c5fb05c46abee7 Content-Type: text/plain; charset="UTF-8" I need something which students and teachers with no professional chemistry background could use as demo lessons of "virtual chemistry". Like a virtual lab. The best analogy is chemistry demonstration in the class by mixing some liquids with a visual result: color change, gas or sediment, etc. In this case the visual effects would be conformation changes or formation of a molecular cluster (temperature down) or cluster evaporation (temperature up). There are plenty movies on youtube of any level of complexity but they would not provide a hands-on experience and ability to change some parameters to get feeling of doing a "chemistry experiment". Best regards, Anatoli Korkin Adjunct Professor School of Molecular Sciences Arizona State University webapp4.asu.edu/directory/person/1169125 President of Nano and Giga Solutions Inc. nanoandgiga.com/board/korkin.html On Wed, Jun 9, 2021 at 7:48 PM Elaine Meng meng{=}cgl.ucsf.edu < owner-chemistry() ccl.net> wrote: > > Sent to CCL by: Elaine Meng [meng-$-cgl.ucsf.edu] > If this is for noncommercial use, you could take a look at the Sophia > plugin to UCSF Chimera; both are free downloads for noncommercial purposes: > > https://www.rbvi.ucsf.edu/chimera/plugins/plugins.html#sophia > https://sophia-web.appspot.com/ > https://www.rbvi.ucsf.edu/chimera/index.html > > However, Sophia may be intended more to teach principles of MD using > simple systems, than to teach chemistry per se. Also developed mainly for > Mac although documentation says most features also work on Windows, and > while it may be easy for you to install, not necessarily so for students. > > Best, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Chimera(X) team > Department of Pharmaceutical Chemistry > University of California, San Francisco > > > > On Jun 9, 2021, at 7:05 AM, Anatoli Korkin korkin-x-nanoandgiga.com > wrote: > > > > > > Sent to CCL by: "Anatoli Korkin" [korkin^nanoandgiga.com] > > I am looking for a free MM/MD program easy to install and operate in > Windows PC > > environment to design some chemistry lessons for high school students, > e.g. > > conformational changes and condensation/evaporation with temperature > change. > > Even better if someone, who is expert in MM/MD, would be interested to > join the > > project and develop some video lessons. See examples on my youtube > channel > > "Atomic Scale Design for Newbies": > > > > https://www.youtube.com/channel/UCQZL1UyyBo7HuN-FA286YWA > > > > Thank you for your advice and consideration! > > > > Sincerely, > > Anatoli Korkin> > > --000000000000d0c5fb05c46abee7 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
I need something which students and teachers with no = professional chemistry background could use as demo lessons of "virtua= l chemistry". Like a virtual lab. The best analogy is chemistry demons= tration in the class by mixing some liquids with a visual result: color cha= nge, gas or sediment, etc. In this case the visual effects would be conform= ation changes or formation of a molecular cluster (temperature down) or clu= ster evaporation (temperature up). There are plenty movies on youtube of an= y level of complexity but they would not provide a hands-on experience and = ability to change some parameters=C2=A0to get feeling of doing a "chem= istry experiment".

Best regards,
Anatoli Kor= kin
Adjunct Professor
=
School of Molecular Sciences
Arizona State University<= /div>
Pr= esident of Nano and Giga Solutions Inc.



On = Wed, Jun 9, 2021 at 7:48 PM Elaine Meng meng{=3D}cgl.ucsf.edu <owner= -chemistry() ccl.net> wrote:

Sent to CCL by: Elaine Meng [meng-$-cgl.ucsf.edu]
If this is for noncommercial use, you could take a look at the Sophia plugi= n to UCSF Chimera; both are free downloads for noncommercial purposes:

https://www.rbvi.ucsf.edu/chimera/plugi= ns/plugins.html#sophia
https://sophia-web.appspot.com/
https://www.rbvi.ucsf.edu/chimera/index.html

However, Sophia may be intended more to teach principles of MD using simple= systems, than to teach chemistry per se.=C2=A0 Also developed mainly for M= ac although documentation says most features also work on Windows, and whil= e it may be easy for you to install, not necessarily so for students.

Best,
Elaine
-----
Elaine C. Meng, Ph.D.=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco


> On Jun 9, 2021, at 7:05 AM, Anatoli Korkin korkin-x-nanoandgiga.= com <owner-chemistry~!~ccl.net> wrote:
>
>
> Sent to CCL by: "Anatoli=C2=A0 Korkin" [korkin^nanoandgiga.com<= /a>]
> I am looking for a free MM/MD program easy to install and operate in W= indows PC
> environment to design some chemistry lessons for high school students,= e.g.
> conformational changes and condensation/evaporation with temperature c= hange.
> Even better if someone, who is expert in MM/MD, would be interested to= join the
> project and develop some video lessons. See examples on my youtube cha= nnel
> "Atomic Scale Design for Newbies":
>
> https://www.youtube.com/channel/UCQZL1U= yyBo7HuN-FA286YWA
>
> Thank you for your advice and consideration!
>
> Sincerely,
> Anatoli Korkin



-=3D This is automatically added to each message by the mailing script =3D-=
E-mail to subscribers: CHEMISTRY() ccl.net or use:
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--000000000000d0c5fb05c46abee7-- From owner-chemistry@ccl.net Thu Jun 10 13:33:00 2021 From: "T. Daniel Crawford crawdad%a%vt.edu" To: CCL Subject: CCL: QM codes NOT written in Fortran Message-Id: <-54380-210610120256-12499-GrLzU+N0/v4gWg7BmapThQ[A]server.ccl.net> X-Original-From: "T. Daniel Crawford" Content-Type: multipart/alternative; boundary="Apple-Mail=_9B72484B-B83B-426D-B8CF-0D3B006829C5" Date: Thu, 10 Jun 2021 12:02:47 -0400 Mime-Version: 1.0 (Mac OS X Mail 14.0 \(3654.100.0.2.22\)) Sent to CCL by: "T. Daniel Crawford" [crawdad=-=vt.edu] --Apple-Mail=_9B72484B-B83B-426D-B8CF-0D3B006829C5 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=utf-8 Psi4 (psicode.org ) is C++ with a Python front end. -TDC -- Prof. T. Daniel Crawford crawdad-.-vt.edu > On Jun 10, 2021, at 12:39 AM, Neese, Frank neese-*-kofo.mpg.de = wrote: >=20 > ORCA is entirely written in C++. AFAIK, MPQC too.=20 >=20 >=20 > Sent from my iPad >=20 >> On 10. Jun 2021, at 03:14, Joe Leonard jleonard42%x%gmail.com = wrote: >>=20 >> =EF=BB=BF Folks, are there QM packages that have managed to = =E2=80=9Close=E2=80=9D all their fortran code or are new enough to have = been developed in a different language or different languages? I have = not seen good comments re: the Mac M1 chipset and I=E2=80=99m curious = whether there are alternatives=E2=80=A6 >>=20 >> I=E2=80=99m sure others would be interested as well. >>=20 >> Joe Leonard >> =E2=80=94 >> "Peter Thiel was right, we just can't build cool sh*t anymore. I = really did want a flying car, and all I have is 140 characters and = promises of AI that never come true." >>=20 --Apple-Mail=_9B72484B-B83B-426D-B8CF-0D3B006829C5 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=utf-8 Psi4 = (psicode.org) is C++ with = a Python front end.

-TDC
--
Prof. T. Daniel Crawford
crawdad-.-vt.edu

On Jun 10, 2021, at 12:39 AM, Neese, Frank neese-*-kofo.mpg.de <owner-chemistry-.-ccl.net> wrote:

ORCA is entirely written in C++. AFAIK, MPQC too. 


Sent from my iPad

On 10. Jun 2021, at 03:14, Joe = Leonard jleonard42%x%gmail.com= <owner-chemistry-.-ccl.net> wrote:

=EF=BB=BF Folks, are there QM packages that = have managed to =E2=80=9Close=E2=80=9D all their fortran code or are new = enough to have been developed in a different language or different = languages?  I have not seen good comments re: the Mac M1 chipset = and I=E2=80=99m curious whether there are alternatives=E2=80=A6

I=E2=80=99m sure others would be interested as = well.

Joe Leonard
=E2=80=94
"Peter Thiel was right, we just can't build cool sh*t anymore. I = really did want a flying car, and all I have is 140 characters = and promises of AI that never come true."


= --Apple-Mail=_9B72484B-B83B-426D-B8CF-0D3B006829C5-- From owner-chemistry@ccl.net Thu Jun 10 14:08:00 2021 From: "Derek Cashman derek.cashman-.-gmail.com" To: CCL Subject: CCL:G: MM/MD program for Windows PC Message-Id: <-54381-210610121831-24546-gXMCZzLqInrV/UxsagF+ow%a%server.ccl.net> X-Original-From: Derek Cashman Content-Type: multipart/alternative; boundary="Apple-Mail=_846BBF7E-DF66-4045-99FB-000E14866703" Date: Thu, 10 Jun 2021 11:18:21 -0500 Mime-Version: 1.0 (Mac OS X Mail 12.4 \(3445.104.17\)) Sent to CCL by: Derek Cashman [derek.cashman^_^gmail.com] --Apple-Mail=_846BBF7E-DF66-4045-99FB-000E14866703 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=utf-8 Avogadro is an excellent and free software for modeling small molecules. = It includes several molecular mechanics force fields, and also has = interfaces for Gaussian, NWChem, and GAMESS for quantum mechanical = calculations as well. I have not used it for molecular dynamics, but = there is an interface to LAMPPS that might be worth investigating as = well. Avogadro can be downloaded for Windows, Mac and Linux here: http://avogadro.cc/ Derek J. Cashman, Ph.D. derek.cashman-.-gmail.com "A drug is any substance which, when injected into a rat, produces a = publishable, scientific paper.=E2=80=9D > On Wed, Jun 9, 2021 at 9:06 AM Anatoli Korkin korkin-x-nanoandgiga.com = > wrote: >=20 > Sent to CCL by: "Anatoli Korkin" [korkin^nanoandgiga.com = ] > I am looking for a free MM/MD program easy to install and operate in = Windows PC=20 > environment to design some chemistry lessons for high school students, = e.g.=20 > conformational changes and condensation/evaporation with temperature = change.=20 > Even better if someone, who is expert in MM/MD, would be interested to = join the=20 > project and develop some video lessons. See examples on my youtube = channel=20 > "Atomic Scale Design for Newbies": >=20 > https://www.youtube.com/channel/UCQZL1UyyBo7HuN-FA286YWA = >=20 > Thank you for your advice and consideration! >=20 > Sincerely, > Anatoli Korkin --Apple-Mail=_846BBF7E-DF66-4045-99FB-000E14866703 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=utf-8
Avogadro is an excellent and free software for modeling small = molecules. It includes several molecular mechanics force fields, and = also has interfaces for Gaussian, NWChem, and GAMESS for quantum = mechanical calculations as well. I have not used it for molecular = dynamics, but there is an interface to LAMPPS that might be worth = investigating as well.

Avogadro can be downloaded for Windows, Mac and Linux = here:

http://avogadro.cc/


Derek J. Cashman, Ph.D.
derek.cashman-.-gmail.com

"A = drug is any substance which, when injected into a rat, produces a = publishable, scientific paper.=E2=80=9D

On Wed, Jun 9, 2021 at 9:06 AM Anatoli Korkin korkin-x-nanoandgiga.com <owner-chemistry%ccl.net> wrote:

Sent to CCL by: "Anatoli  Korkin" [korkin^nanoandgiga.com]
I am looking for a free MM/MD program easy to install and operate in = Windows PC
environment to design some chemistry lessons for high school students, = e.g.
conformational changes and condensation/evaporation with temperature = change.
Even better if someone, who is expert in MM/MD, would be interested to = join the
project and develop some video lessons. See examples on my youtube = channel
"Atomic Scale Design for Newbies":

https://www.youtube.com/channel/UCQZL1UyyBo7HuN-FA286YWA
Thank you for your advice and consideration!

Sincerely,
Anatoli Korkin

= --Apple-Mail=_846BBF7E-DF66-4045-99FB-000E14866703-- From owner-chemistry@ccl.net Thu Jun 10 14:43:00 2021 From: "Joseph Leonard jleonard42!A!gmail.com" To: CCL Subject: CCL: MM/MD program for Windows PC Message-Id: <-54382-210610140900-19064-c/WcIdgzTEgeJN1atD31rg .. server.ccl.net> X-Original-From: Joseph Leonard Content-Type: multipart/alternative; boundary="000000000000b29d4e05c46d48f9" Date: Thu, 10 Jun 2021 14:08:43 -0400 MIME-Version: 1.0 Sent to CCL by: Joseph Leonard [jleonard42_-_gmail.com] --000000000000b29d4e05c46d48f9 Content-Type: text/plain; charset="UTF-8" You might want to look at the educational offerings from Wavefunction ( www.wavefun.com). They also wrote experimental books as I recall. Joe Leonard On Thu, Jun 10, 2021 at 2:04 PM Anatoli Korkin korkin.++.nanoandgiga.com < owner-chemistry++ccl.net> wrote: > I need something which students and teachers with no professional > chemistry background could use as demo lessons of "virtual chemistry". Like > a virtual lab. The best analogy is chemistry demonstration in the class by > mixing some liquids with a visual result: color change, gas or sediment, > etc. In this case the visual effects would be conformation changes or > formation of a molecular cluster (temperature down) or cluster evaporation > (temperature up). There are plenty movies on youtube of any level of > complexity but they would not provide a hands-on experience and ability to > change some parameters to get feeling of doing a "chemistry experiment". > > Best regards, > Anatoli Korkin > Adjunct Professor > School of Molecular Sciences > Arizona State University > webapp4.asu.edu/directory/person/1169125 > President of Nano and Giga Solutions Inc. > nanoandgiga.com/board/korkin.html > > > > On Wed, Jun 9, 2021 at 7:48 PM Elaine Meng meng{=}cgl.ucsf.edu < > owner-chemistry#%#ccl.net> wrote: > >> >> Sent to CCL by: Elaine Meng [meng-$-cgl.ucsf.edu] >> If this is for noncommercial use, you could take a look at the Sophia >> plugin to UCSF Chimera; both are free downloads for noncommercial purposes: >> >> https://www.rbvi.ucsf.edu/chimera/plugins/plugins.html#sophia >> https://sophia-web.appspot.com/ >> https://www.rbvi.ucsf.edu/chimera/index.html >> >> However, Sophia may be intended more to teach principles of MD using >> simple systems, than to teach chemistry per se. Also developed mainly for >> Mac although documentation says most features also work on Windows, and >> while it may be easy for you to install, not necessarily so for students. >> >> Best, >> Elaine >> ----- >> Elaine C. Meng, Ph.D. >> UCSF Chimera(X) team >> Department of Pharmaceutical Chemistry >> University of California, San Francisco >> >> >> > On Jun 9, 2021, at 7:05 AM, Anatoli Korkin korkin-x-nanoandgiga.com >> wrote: >> > >> > >> > Sent to CCL by: "Anatoli Korkin" [korkin^nanoandgiga.com] >> > I am looking for a free MM/MD program easy to install and operate in >> Windows PC >> > environment to design some chemistry lessons for high school students, >> e.g. >> > conformational changes and condensation/evaporation with temperature >> change. >> > Even better if someone, who is expert in MM/MD, would be interested to >> join the >> > project and develop some video lessons. See examples on my youtube >> channel >> > "Atomic Scale Design for Newbies": >> > >> > https://www.youtube.com/channel/UCQZL1UyyBo7HuN-FA286YWA >> > >> > Thank you for your advice and consideration! >> > >> > Sincerely, >> > Anatoli Korkin>> E-mail to subscribers: CHEMISTRY#%#ccl.net or use:>> >> E-mail to administrators: CHEMISTRY-REQUEST#%#ccl.net or use>> >> >> -- -- "Peter Thiel was right, we just can't build cool sh*t anymore. I really did want a flying car, and all I have is 140 characters and promises of AI that never come true." --000000000000b29d4e05c46d48f9 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
You might want to look at the educational offerings from = Wavefunction (www.wavefun.com).=C2= =A0 They also wrote experimental books as I recall.
=
Joe Leonard=C2=A0

On Thu, Jun 10, 2021 at 2= :04 PM Anatoli Korkin korkin.++.nanoandgi= ga.com <owner-chemistry++c= cl.net> wrote:
I need something which students and teachers with no professional = chemistry background could use as demo lessons of "virtual chemistry&q= uot;. Like a virtual lab. The best analogy is chemistry demonstration in th= e class by mixing some liquids with a visual result: color change, gas or s= ediment, etc. In this case the visual effects would be conformation changes= or formation of a molecular cluster (temperature down) or cluster evaporat= ion (temperature up). There are plenty movies on youtube of any level of co= mplexity but they would not provide a hands-on experience and ability to ch= ange some parameters=C2=A0to get feeling of doing a "chemistry experim= ent".

Best regards,
Anatoli Korkin
Adjunct Professor
School of Molecular Sciences
Arizona State University
President of Nano and Giga Solutions Inc.

=


On Wed, Jun 9, 2021 at 7:48 PM Elaine Meng m= eng{=3D}cgl.ucsf.edu = <owne= r-chemistry#%#ccl.net> wrote:

Sent to CCL by: Elaine Meng [meng-$-cgl.ucsf.edu]
If this is for noncommercial use, you could take a look at the Sophia plugi= n to UCSF Chimera; both are free downloads for noncommercial purposes:

https://www.rbvi.ucsf.edu/chimera/plugi= ns/plugins.html#sophia
https://sophia-web.appspot.com/
https://www.rbvi.ucsf.edu/chimera/index.html

However, Sophia may be intended more to teach principles of MD using simple= systems, than to teach chemistry per se.=C2=A0 Also developed mainly for M= ac although documentation says most features also work on Windows, and whil= e it may be easy for you to install, not necessarily so for students.

Best,
Elaine
-----
Elaine C. Meng, Ph.D.=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco


> On Jun 9, 2021, at 7:05 AM, Anatoli Korkin korkin-x-nanoandgiga.= com <owner-chemistry~!~ccl.net> wrote:
>
>
> Sent to CCL by: "Anatoli=C2=A0 Korkin" [korkin^nanoandgiga.com<= /a>]
> I am looking for a free MM/MD program easy to install and operate in W= indows PC
> environment to design some chemistry lessons for high school students,= e.g.
> conformational changes and condensation/evaporation with temperature c= hange.
> Even better if someone, who is expert in MM/MD, would be interested to= join the
> project and develop some video lessons. See examples on my youtube cha= nnel
> "Atomic Scale Design for Newbies":
>
> https://www.youtube.com/channel/UCQZL1U= yyBo7HuN-FA286YWA
>
> Thank you for your advice and consideration!
>
> Sincerely,
> Anatoli Korkin



-=3D This is automatically added to each message by the mailing script =3D-=
E-mail to subscribers: CHEMISTRY#%#ccl.net or use:
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Before posting, check wait time at: http://www.ccl.net

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Conferences: http://server.ccl.net/chemist= ry/announcements/conferences/

Search Messages: http://www.ccl.net/chemistry/sear= chccl/index.shtml
=C2=A0 =C2=A0 =C2=A0 http://www.ccl.net/spammers.txt

RTFI: http://www.ccl.net/chemistry/aboutccl/ins= tructions/


--
--
"Peter= Thiel was right, we just can't build cool sh*t anymore. I really did w= ant a flying car, and all I have is 140 characters and promises of AI that = never come true."
--000000000000b29d4e05c46d48f9-- From owner-chemistry@ccl.net Thu Jun 10 15:33:00 2021 From: "Eyringpy Team eyringpy2018(~)gmail.com" To: CCL Subject: CCL: Eyringpy Software Message-Id: <-54383-210610143946-14085-+/Nxz4BN9qsQ7Nzo7DWrVA*server.ccl.net> X-Original-From: "Eyringpy Team" Date: Thu, 10 Jun 2021 14:39:44 -0400 Sent to CCL by: "Eyringpy Team" [eyringpy2018%a%gmail.com] Dear all, We are glad to share with you Eyringpy. It is a program for computing rate constants (https://doi.org/10.1002/qua.25686) and monitoring primitive properties along the intrinsic reaction coordinate (IRC) (https://doi.org/10.1002/qua.26684). If you are interested in Eyringpy, visit our web page: https://www.theochemmerida.org/eyringpy Best regards, The Eyringpy team Eyringpy Team Departamento de Fisica Aplicada Centro de Investigacion y de Estudios Avanzados Unidad Merida Km. 6 Antigua carretera a Progreso Apdo. Postal 73, Cordemex, 97310, Mrida, Yuc., Mxico e-mail: eyringpy2018-.-gmail.com From owner-chemistry@ccl.net Thu Jun 10 16:42:01 2021 From: "Brian Skinn brian.skinn : gmail.com" To: CCL Subject: CCL: MM/MD program for Windows PC Message-Id: <-54384-210610153727-31080-ftJKOUwlFLBFyDKJ/RP3bg * server.ccl.net> X-Original-From: Brian Skinn Content-Type: multipart/alternative; boundary="0000000000000761e805c46e8574" Date: Thu, 10 Jun 2021 15:37:09 -0400 MIME-Version: 1.0 Sent to CCL by: Brian Skinn [brian.skinn::gmail.com] --0000000000000761e805c46e8574 Content-Type: text/plain; charset="UTF-8" Anatoli, I did a quick Google search for "interactive molecular model of condensation", and discovered this: http://mw.concord.org/nextgen/ I have no experience with them at all, and cannot make any particular recommendation. The demonstration on the landing page seems exactly like what you describe, though. I'm not sure how you would go about making use of their product...it might involve becoming one of their "partners"? Good luck, Brian On Thu, Jun 10, 2021 at 3:30 PM Anatoli Korkin korkin.^^^.nanoandgiga.com < owner-chemistry^^^ccl.net> wrote: > I need something which students and teachers with no professional > chemistry background could use as demo lessons of "virtual chemistry". Like > a virtual lab. The best analogy is chemistry demonstration in the class by > mixing some liquids with a visual result: color change, gas or sediment, > etc. In this case the visual effects would be conformation changes or > formation of a molecular cluster (temperature down) or cluster evaporation > (temperature up). There are plenty movies on youtube of any level of > complexity but they would not provide a hands-on experience and ability to > change some parameters to get feeling of doing a "chemistry experiment". > > Best regards, > Anatoli Korkin > Adjunct Professor > School of Molecular Sciences > Arizona State University > webapp4.asu.edu/directory/person/1169125 > President of Nano and Giga Solutions Inc. > nanoandgiga.com/board/korkin.html > > > > On Wed, Jun 9, 2021 at 7:48 PM Elaine Meng meng{=}cgl.ucsf.edu < > owner-chemistry#%#ccl.net> wrote: > >> >> Sent to CCL by: Elaine Meng [meng-$-cgl.ucsf.edu] >> If this is for noncommercial use, you could take a look at the Sophia >> plugin to UCSF Chimera; both are free downloads for noncommercial purposes: >> >> https://www.rbvi.ucsf.edu/chimera/plugins/plugins.html#sophia >> https://sophia-web.appspot.com/ >> https://www.rbvi.ucsf.edu/chimera/index.html >> >> However, Sophia may be intended more to teach principles of MD using >> simple systems, than to teach chemistry per se. Also developed mainly for >> Mac although documentation says most features also work on Windows, and >> while it may be easy for you to install, not necessarily so for students. >> >> Best, >> Elaine >> ----- >> Elaine C. Meng, Ph.D. >> UCSF Chimera(X) team >> Department of Pharmaceutical Chemistry >> University of California, San Francisco >> >> >> > On Jun 9, 2021, at 7:05 AM, Anatoli Korkin korkin-x-nanoandgiga.com >> wrote: >> > >> > >> > Sent to CCL by: "Anatoli Korkin" [korkin^nanoandgiga.com] >> > I am looking for a free MM/MD program easy to install and operate in >> Windows PC >> > environment to design some chemistry lessons for high school students, >> e.g. >> > conformational changes and condensation/evaporation with temperature >> change. >> > Even better if someone, who is expert in MM/MD, would be interested to >> join the >> > project and develop some video lessons. See examples on my youtube >> channel >> > "Atomic Scale Design for Newbies": >> > >> > https://www.youtube.com/channel/UCQZL1UyyBo7HuN-FA286YWA >> > >> > Thank you for your advice and consideration! >> > >> > Sincerely, >> > Anatoli Korkin>> E-mail to subscribers: CHEMISTRY#%#ccl.net or use:>> >> E-mail to administrators: CHEMISTRY-REQUEST#%#ccl.net or use>> >> >> --0000000000000761e805c46e8574 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Anatoli,

I did a quick Google search fo= r "interactive molecular model of condensation", and discovered t= his:=C2=A0http://mw.concord.org/= nextgen/

I have no experience with them at all= , and cannot make any particular recommendation. The demonstration on the l= anding page seems exactly like what you describe, though. I'm not sure = how you would go about making use of their product...it might involve becom= ing=C2=A0one of their "partners"?


Good luck,
Brian

On Thu, Jun 10, 2021 at 3:30 PM An= atoli Korkin korkin.^^^.nanoandgiga.com <owner-chemistry^^^ccl.net> wrote:
I need something which students and teachers with no pro= fessional chemistry background could use as demo lessons of "virtual c= hemistry". Like a virtual lab. The best analogy is chemistry demonstra= tion in the class by mixing some liquids with a visual result: color change= , gas or sediment, etc. In this case the visual effects would be conformati= on changes or formation of a molecular cluster (temperature down) or cluste= r evaporation (temperature up). There are plenty movies on youtube of any l= evel of complexity but they would not provide a hands-on experience and abi= lity to change some parameters=C2=A0to get feeling of doing a "chemist= ry experiment".


On Wed, Jun 9, 2021 at 7:48 PM Elaine Meng meng{=3D}cgl.ucsf.edu <owner-chemistry#%#ccl.net> wrote:
Sent to CCL by: Elaine Meng [meng-$-cgl.ucsf.edu]
If this is for noncommercial use, you could take a look at the Sophia plugi= n to UCSF Chimera; both are free downloads for noncommercial purposes:

https://www.rbvi.ucsf.edu/chimera/plugi= ns/plugins.html#sophia
https://sophia-web.appspot.com/
https://www.rbvi.ucsf.edu/chimera/index.html

However, Sophia may be intended more to teach principles of MD using simple= systems, than to teach chemistry per se.=C2=A0 Also developed mainly for M= ac although documentation says most features also work on Windows, and whil= e it may be easy for you to install, not necessarily so for students.

Best,
Elaine
-----
Elaine C. Meng, Ph.D.=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco


> On Jun 9, 2021, at 7:05 AM, Anatoli Korkin korkin-x-nanoandgiga.= com <owner-chemistry~!~ccl.net> wrote:
>
>
> Sent to CCL by: "Anatoli=C2=A0 Korkin" [korkin^nanoandgiga.com<= /a>]
> I am looking for a free MM/MD program easy to install and operate in W= indows PC
> environment to design some chemistry lessons for high school students,= e.g.
> conformational changes and condensation/evaporation with temperature c= hange.
> Even better if someone, who is expert in MM/MD, would be interested to= join the
> project and develop some video lessons. See examples on my youtube cha= nnel
> "Atomic Scale Design for Newbies":
>
> https://www.youtube.com/channel/UCQZL1U= yyBo7HuN-FA286YWA
>
> Thank you for your advice and consideration!
>
> Sincerely,
> Anatoli Korkin



-=3D This is automatically added to each message by the mailing script =3D-=
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--0000000000000761e805c46e8574-- From owner-chemistry@ccl.net Thu Jun 10 17:17:00 2021 From: "Chris Swain swain[-]mac.com" To: CCL Subject: CCL: MM/MD program for Windows PC Message-Id: <-54385-210610154537-5404-QYz9EfEQswUHZnTkqbt9iw]|[server.ccl.net> X-Original-From: Chris Swain Content-Type: multipart/alternative; boundary="Apple-Mail=_3032C608-7146-47DE-9CAF-B122404BFD59" Date: Thu, 10 Jun 2021 20:45:29 +0100 Mime-Version: 1.0 (Mac OS X Mail 14.0 \(3654.100.0.2.22\)) Sent to CCL by: Chris Swain [swain^mac.com] --Apple-Mail=_3032C608-7146-47DE-9CAF-B122404BFD59 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=us-ascii Perhaps something like https://www.youtube.com/watch?v=3DKEIpJ50Jc0w = Cheers, Chris > On 10 Jun 2021, at 16:06, Anatoli Korkin korkin. a .nanoandgiga.com = wrote: >=20 > I need something which students and teachers with no professional = chemistry background could use as demo lessons of "virtual chemistry". = Like a virtual lab. The best analogy is chemistry demonstration in the = class by mixing some liquids with a visual result: color change, gas or = sediment, etc. In this case the visual effects would be conformation = changes or formation of a molecular cluster (temperature down) or = cluster evaporation (temperature up). There are plenty movies on youtube = of any level of complexity but they would not provide a hands-on = experience and ability to change some parameters to get feeling of doing = a "chemistry experiment". >=20 > Best regards, > Anatoli Korkin > Adjunct Professor > School of Molecular Sciences > Arizona State University > webapp4.asu.edu/directory/person/1169125 = > President of Nano and Giga Solutions Inc. > nanoandgiga.com/board/korkin.html = >=20 >=20 >=20 > On Wed, Jun 9, 2021 at 7:48 PM Elaine Meng meng{=3D}cgl.ucsf.edu = > wrote: >=20 > Sent to CCL by: Elaine Meng [meng-$-cgl.ucsf.edu = ] > If this is for noncommercial use, you could take a look at the Sophia = plugin to UCSF Chimera; both are free downloads for noncommercial = purposes: >=20 > https://www.rbvi.ucsf.edu/chimera/plugins/plugins.html#sophia = > https://sophia-web.appspot.com/ > https://www.rbvi.ucsf.edu/chimera/index.html = >=20 > However, Sophia may be intended more to teach principles of MD using = simple systems, than to teach chemistry per se. Also developed mainly = for Mac although documentation says most features also work on Windows, = and while it may be easy for you to install, not necessarily so for = students. >=20 > Best, > Elaine > ----- > Elaine C. Meng, Ph.D. =20 > UCSF Chimera(X) team > Department of Pharmaceutical Chemistry > University of California, San Francisco >=20 >=20 > > On Jun 9, 2021, at 7:05 AM, Anatoli Korkin korkin-x-nanoandgiga.com = > wrote: > >=20 > >=20 > > Sent to CCL by: "Anatoli Korkin" [korkin^nanoandgiga.com = ] > > I am looking for a free MM/MD program easy to install and operate in = Windows PC=20 > > environment to design some chemistry lessons for high school = students, e.g.=20 > > conformational changes and condensation/evaporation with temperature = change.=20 > > Even better if someone, who is expert in MM/MD, would be interested = to join the=20 > > project and develop some video lessons. See examples on my youtube = channel=20 > > "Atomic Scale Design for Newbies": > >=20 > > https://www.youtube.com/channel/UCQZL1UyyBo7HuN-FA286YWA = > >=20 > > Thank you for your advice and consideration! > >=20 > > Sincerely, > > Anatoli Korkin >=20 >=20 >=20 > -=3D This is automatically added to each message by the mailing script = =3D- >=20 >=20 >=20 > E-mail to subscribers: CHEMISTRY#%#ccl.net = or use:= >=20 > E-mail to administrators: CHEMISTRY-REQUEST#%#ccl.net = or use= >=20 >=20= >=20= >=20=20 > Conferences: = http://server.ccl.net/chemistry/announcements/conferences/ = >=20= >=20 >=20= >=20= >=20 >=20 --Apple-Mail=_3032C608-7146-47DE-9CAF-B122404BFD59 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=us-ascii Perhaps something like

https://www.youtube.com/watch?v=3DKEIpJ50Jc0w

Cheers,

Chris

On 10 Jun 2021, at 16:06, Anatoli Korkin korkin. a .nanoandgiga.com <owner-chemistry a ccl.net> wrote:

I need something which students and teachers = with no professional chemistry background could use as demo lessons of = "virtual chemistry". Like a virtual lab. The best analogy is chemistry = demonstration in the class by mixing some liquids with a visual result: = color change, gas or sediment, etc. In this case the visual effects = would be conformation changes or formation of a molecular cluster = (temperature down) or cluster evaporation (temperature up). There are = plenty movies on youtube of any level of complexity but they would not = provide a hands-on experience and ability to change some = parameters to get feeling of doing a "chemistry = experiment".

Best regards,
Anatoli = Korkin
Adjunct Professor
School of Molecular Sciences
Arizona = State University
webapp4.asu.edu/directory/person/1169125
President of Nano and Giga Solutions = Inc.
nanoandgiga.com/board/korkin.html



On Wed, Jun 9, 2021 at 7:48 PM Elaine = Meng meng{=3D}cgl.ucsf.edu= <owner-chemistry#%#ccl.net> wrote:

Sent to CCL by: Elaine Meng [meng-$-cgl.ucsf.edu]
If this is for noncommercial use, you could take a look at the Sophia = plugin to UCSF Chimera; both are free downloads for noncommercial = purposes:

https://www.rbvi.ucsf.edu/chimera/plugins/plugins.html#sophia
https://sophia-web.appspot.com/
https://www.rbvi.ucsf.edu/chimera/index.html
=
However, Sophia may be intended more to teach principles of MD using = simple systems, than to teach chemistry per se.  Also developed = mainly for Mac although documentation says most features also work on = Windows, and while it may be easy for you to install, not necessarily so = for students.

Best,
Elaine
-----
Elaine C. Meng, Ph.D.              =          
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco


> On Jun 9, 2021, at 7:05 AM, Anatoli Korkin korkin-x-nanoandgiga.com = <owner-chemistry~!~ccl.net> wrote:
>
>
> Sent to CCL by: "Anatoli  Korkin" [korkin^nanoandgiga.com]
> I am looking for a free MM/MD program easy to install and operate = in Windows PC
> environment to design some chemistry lessons for high school = students, e.g.
> conformational changes and condensation/evaporation with = temperature change.
> Even better if someone, who is expert in MM/MD, would be interested = to join the
> project and develop some video lessons. See examples on my youtube = channel
> "Atomic Scale Design for Newbies":
>
> https://www.youtube.com/channel/UCQZL1UyyBo7HuN-FA286YWA >
> Thank you for your advice and consideration!
>
> Sincerely,
> Anatoli Korkin



-=3D This is automatically added to each message by the mailing script = =3D-



E-mail to subscribers: CHEMISTRY#%#ccl.net or use:
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=
Before posting, check wait time at: http://www.ccl.net

Job: http://www.ccl.net/jobs
Conferences: http://server.ccl.net/chemistry/announcements/conferences/<= br class=3D"">
Search Messages: http://www.ccl.net/chemistry/searchccl/index.shtml


      http://www.ccl.net/spammers.txt

RTFI: http://www.ccl.net/chemistry/aboutccl/instructions/



= --Apple-Mail=_3032C608-7146-47DE-9CAF-B122404BFD59-- From owner-chemistry@ccl.net Thu Jun 10 18:12:01 2021 From: "j j robinson jameschums(~)yahoo.com" To: CCL Subject: CCL: QM codes NOT written in Fortran Message-Id: <-54386-210610151033-9931-P3RENa6VuXhxkNktFtUtQw()server.ccl.net> X-Original-From: j j robinson Content-Type: multipart/alternative; boundary="----=_Part_5918157_524030674.1623352181046" Date: Thu, 10 Jun 2021 19:09:41 +0000 (UTC) MIME-Version: 1.0 Sent to CCL by: j j robinson [jameschums#%#yahoo.com] ------=_Part_5918157_524030674.1623352181046 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Dear Jurgen and Phil,=20 other reasons for choosing Fortran is good memory allocation/deallocation, = lapack/64, openmpi. I worked as a C++ coder for a while and trying to under= stand boost, armadillo and polymorphism made my head hurt. Lapack is a good= numerical library. I also quite likenumpy-f2py. Fortran is for scone-cream= -then jam, whereas C++ might be scone-jam then cream; it does come down to = personal preferences. I have just found fortran to be easier to understand = over the years. I also understand if students want to learn C++ for employa= bility. Enjoy your scones, however you code them.=20 Met vriendelijke groet / mit freundlichen Gr=C3=BC=C3=9Fen / kind regards= =20 J J Robinson - personal email - opinions are personal only.=20 On Thursday, 10 June 2021, 20:44:10 CEST, Phil Hasnip phil.hasnip~~york= .ac.uk wrote: =20 =20 Dear=C2=A0J=C3=BCrgen, Thank you, I intended to write Python/C but clearly my brain did not commun= icate that to my fingers! I appreciate you correcting me. Not that you can'= t write a QM program entirely in Python, but the performance would be too p= oor to use in any research context. All the best, Phil ---------------------------------------------------------------------------= --------- Dr Phil Hasnip =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0=C2=A0=C2=A0=C2=A0= =C2=A0=C2=A0 Email: phil.hasnip|a|york.ac.uk EPSRC RSE Fellow=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 Web:=C2=A0= www-users.york.ac.uk/~pjh503 Dept of Physics University of York =C2=A0 =C2=A0 =C2=A0 =C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 Tel:= =C2=A0=C2=A0=C2=A0 +44 (0)1904 322225 York YO10 5DD On Thu, 10 Jun 2021 at 09:47, J=C3=BCrgen Gr=C3=A4fenstein jurgen.grafenste= in#%#chem.gu.se wrote: Dear Phil, GPAW is actually written in a combination of C (for the hard-core part) and= Python (for the high-level layer). You can find more information here: https://www.sciencedirect.com/science/article/pii/S1877050911000615 Best regards,J=C3=BCrgen _____________________________________J=C3=BCrgen Gr=C3=A4fensteinUniversity= of GothenburgDept of Chemistry and Molecular BiologySE-412 96 G=C3=B6tebor= gSweden jurgen.grafenstein|a|chem.gu.se On 10 Jun 2021, at 04:07, Phil Hasnip phil.hasnip[-]york.ac.uk wrote: Dear Joe, Yes there are, for example GPAW is written in Python. However, the choice o= f many QM programs to use Fortran is not simply because they=C2=A0are "old"= codes, many newer QM packages have deliberately chosen Fortran over altern= atives (e.g. C++). QM simulations are computationally intensive, and Fortra= n is rather hard to beat performance-wise -- though modern C++ compilers ar= e competitive these days (albeit with compiler development teams an order o= f magnitude larger than the corresponding Fortran ones). Fortran also has m= any modern features which are still lacking in most mainstream languages, f= or example partitioned global-address space (coarrays).=C2=A0 I don't see much incentive to move the millions of lines of Fortran into an= other language, but what is becoming increasingly common is to develop a hi= gh-level software layer in something else, usually Python, which allows mor= e rapid prototyping and development, whilst keeping all the numerically-int= ensive work in Fortran or C++. I'm confused about your Mac M1 chipset reference; how does this relate to y= our Fortran question? There are good ARM Fortran compilers, if that's what = you're worried about.=C2=A0 All the best, Phil Hasnip ---------------------------------------------------------------------------= --------- Dr Phil Hasnip =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0=C2=A0=C2=A0=C2=A0= =C2=A0=C2=A0 Email: phil.hasnip**york.ac.uk EPSRC RSE Fellow=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 Web:=C2=A0= www-users.york.ac.uk/~pjh503 Dept of Physics University of York =C2=A0 =C2=A0 =C2=A0 =C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 Tel:= =C2=A0=C2=A0=C2=A0 +44 (0)1904 322225 York YO10 5DD On Thu, 10 Jun 2021 at 01:58, Joe Leonard jleonard42%x%gmail.com wrote: Folks, are there QM packages that have managed to =E2=80=9Close=E2=80=9D al= l their fortran code or are new enough to have been developed in a differen= t language or different languages?=C2=A0 I have not seen good comments re: = the Mac M1 chipset and I=E2=80=99m curious whether there are alternatives= =E2=80=A6 I=E2=80=99m sure others would be interested as well. Joe Leonard=E2=80=94"Peter Thiel was right, we just can't build=C2=A0cool s= h*t anymore. I really did want a=C2=A0flying car, and all I have is 140=C2= =A0characters and promises of AI that never=C2=A0come true." =20 ------=_Part_5918157_524030674.1623352181046 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Dear Jurgen and Phil,

other reasons for choosing Fortran is good memory allocati= on/deallocation, lapack/64, openmpi. I worked as a C++ coder for a while an= d trying to understand boost, armadillo and polymorphism made my head hurt.= Lapack is a good numerical library. I also quite likenumpy-f2py. Fortran i= s for scone-cream-then jam, whereas C++ might be scone-jam then cream; it d= oes come down to personal preferences. I have just found fortran to be easi= er to understand over the years. I also understand if students want to lear= n C++ for employability. Enjoy your scones, however you code them.

Met vri= endelijke groet / mit freundlichen Gr=C3=BC=C3=9Fen / kind regards

J J Robinson - personal email - opinions = are personal only.


=20
=20
On Thursday, 10 June 2021, 20:44:10 CEST, Phil Hasnip p= hil.hasnip~~york.ac.uk <owner-chemistry:_:ccl.net> wrote:


Dear J=C3=BCrgen,

Thank you, I = intended to write Python/C but clearly my brain did not communicate that to= my fingers! I appreciate you correcting me. Not that you can't write a QM = program entirely in Python, but the performance would be too poor to use in= any research context.

All the best= ,

Phil

=
--------------------------------------------------------= ----------------------------
Dr Phil Hasnip    =              Email: phil.hasnip|a|york.ac.uk
EPSRC RSE Fellow=          Web:  www-users.york.ac.uk/~pjh503
Dept of Physics<= br clear=3D"none">University of York          = ;   Tel:     +44 (0)1904 322225
= York YO10 5DD

=

On Thu= , 10 Jun 2021 at 09:47, J=C3=BCrgen Gr=C3=A4fenstein jurgen.grafenstein#%#<= a shape=3D"rect" href=3D"http://chem.gu.se" rel=3D"nofollow" target=3D"_bla= nk">chem.gu.se <owner-chemistry|a|ccl.net>= ; wrote:
Dear Phil,

GPAW is actually written in a combination of C (for the hard-core part= ) and Python (for the high-level layer). You can find more information here= :


Best regards,
J=C3=BCrgen

_____________________________________
J=C3=BCrgen Gr=C3=A4fenstein
University of Gothenburg
Dept of Chemistry and Molecular Biology
SE-412 96 G=C3=B6teborg
Sweden

jurgen.grafenstein|a|chem.gu.se

On 10 Jun 2021, at 04:07, Phil Hasnip phil.hasnip[-]york.ac.uk <owner-chemistry|a|ccl.net> wrote:

Dear Joe,

Yes there are, for example GPAW is written in Python. However, the cho= ice of many QM programs to use Fortran is not simply because they are = "old" codes, many newer QM packages have deliberately chosen Fortran over a= lternatives (e.g. C++). QM simulations are computationally intensive, and Fortran is rather hard to beat performa= nce-wise -- though modern C++ compilers are competitive these days (albeit = with compiler development teams an order of magnitude larger than the corre= sponding Fortran ones). Fortran also has many modern features which are still lacking in most mainstream l= anguages, for example partitioned global-address space (coarrays). 

I don't see much incentive to move the millions of lines of Fortran in= to another language, but what is becoming increasingly common is to develop= a high-level software layer in something else, usually Python, which allow= s more rapid prototyping and development, whilst keeping all the numerically-intensive work in Fort= ran or C++.

I'm confused about your Mac M1 chipset reference; how does this relate to y= our Fortran question? There are good ARM Fortran compilers, if that's what = you're worried about. 

All the best,

Phil Hasnip

----------------------------------------------------------------------= --------------
Dr Phil Hasnip               &= nbsp;  Email: phil.hasnip**york.ac.uk
EPSRC RSE Fellow         Web: = www-users.york.ac.uk/~pjh503
Dept of Physics
University of York             Tel:=     +44 (0)1904 322225
York YO10 5DD


On Thu, 10 Ju= n 2021 at 01:58, Joe Leonard jleonard42%x%gmail.com <owner-chemistry**ccl.net> wrote:
Folks, are there QM packages that have managed to =E2=80=9Close=E2=80= =9D all their fortran code or are new enough to have been developed in a di= fferent language or different languages?  I have not seen good comment= s re: the Mac M1 chipset and I=E2=80=99m curious whether there are alternatives=E2= =80=A6

I=E2=80=99m sure others would be interested as well.

Joe Leonard
=E2=80=94
"Peter Thiel was right, we just can't build=  cool sh*t anymore. I really did want a flying car, and all I hav= e is 140 characters and promises of AI that never come true."


------=_Part_5918157_524030674.1623352181046-- From owner-chemistry@ccl.net Thu Jun 10 18:47:01 2021 From: "Alan Shusterman alan[a]reed.edu" To: CCL Subject: CCL: MM/MD program for Windows PC Message-Id: <-54387-210610164855-15671-DWrmXP4qj6KvEROka8wleg===server.ccl.net> X-Original-From: Alan Shusterman Content-Type: multipart/alternative; boundary="00000000000075ad8c05c46f8431" Date: Thu, 10 Jun 2021 13:48:34 -0700 MIME-Version: 1.0 Sent to CCL by: Alan Shusterman [alan!=!reed.edu] --00000000000075ad8c05c46f8431 Content-Type: text/plain; charset="UTF-8" > ... Like a virtual lab. ... There are plenty movies on youtube of any level of complexity but they would not provide a hands-on experience and ability to change some parameters to get feeling of doing a "chemistry experiment". I understand and endorse what you are saying. Being able to "play" with a model (experiment) and see how the observables respond to adjustments in parameters and/or molecular composition/structure is exactly what Odyssey is designed to do. Also, not only does it contain multiple *experiments*, most of these experiments provide students with a set of compounds to investigate. Odyssey's presentation of the simulation is also much richer than any movie is likely to be. There are a number of easy-to-use tools that take the user more deeply into the visualizations, e.g., atom tools, tools for focusing on particular sets of atoms, much more. And, beyond visuation itself, there are tools in the software for gathering/displaying numerical data (graphs, charts) about the simulation. Like I said, Odyssey is not free. I've purchased a campus-wide site license in the past to make Odyssey available to all students on my campus. But I suggest you "try before you buy". Request a demo trial. You can then follow the tutorials provided with the software, and whenever you're ready, jump into the large number of models that are provided. And, like I said, even if you don't go this route, I think you'll find a lot in Odyssey that inspires you in whatever direction you go. Good luck! Alan On Thu, Jun 10, 2021 at 11:24 AM Anatoli Korkin korkin.-#-.nanoandgiga.com < owner-chemistry-#-ccl.net> wrote: > I need something which students and teachers with no professional > chemistry background could use as demo lessons of "virtual chemistry". Like > a virtual lab. The best analogy is chemistry demonstration in the class by > mixing some liquids with a visual result: color change, gas or sediment, > etc. In this case the visual effects would be conformation changes or > formation of a molecular cluster (temperature down) or cluster evaporation > (temperature up). There are plenty movies on youtube of any level of > complexity but they would not provide a hands-on experience and ability to > change some parameters to get feeling of doing a "chemistry experiment". > > Best regards, > Anatoli Korkin > Adjunct Professor > School of Molecular Sciences > Arizona State University > webapp4.asu.edu/directory/person/1169125 > President of Nano and Giga Solutions Inc. > nanoandgiga.com/board/korkin.html > > > > On Wed, Jun 9, 2021 at 7:48 PM Elaine Meng meng{=}cgl.ucsf.edu < > owner-chemistry#%#ccl.net> wrote: > >> >> Sent to CCL by: Elaine Meng [meng-$-cgl.ucsf.edu] >> If this is for noncommercial use, you could take a look at the Sophia >> plugin to UCSF Chimera; both are free downloads for noncommercial purposes: >> >> https://www.rbvi.ucsf.edu/chimera/plugins/plugins.html#sophia >> https://sophia-web.appspot.com/ >> https://www.rbvi.ucsf.edu/chimera/index.html >> >> However, Sophia may be intended more to teach principles of MD using >> simple systems, than to teach chemistry per se. Also developed mainly for >> Mac although documentation says most features also work on Windows, and >> while it may be easy for you to install, not necessarily so for students. >> >> Best, >> Elaine >> ----- >> Elaine C. Meng, Ph.D. >> UCSF Chimera(X) team >> Department of Pharmaceutical Chemistry >> University of California, San Francisco >> >> >> > On Jun 9, 2021, at 7:05 AM, Anatoli Korkin korkin-x-nanoandgiga.com >> wrote: >> > >> > >> > Sent to CCL by: "Anatoli Korkin" [korkin^nanoandgiga.com] >> > I am looking for a free MM/MD program easy to install and operate in >> Windows PC >> > environment to design some chemistry lessons for high school students, >> e.g. >> > conformational changes and condensation/evaporation with temperature >> change. >> > Even better if someone, who is expert in MM/MD, would be interested to >> join the >> > project and develop some video lessons. See examples on my youtube >> channel >> > "Atomic Scale Design for Newbies": >> > >> > https://www.youtube.com/channel/UCQZL1UyyBo7HuN-FA286YWA >> > >> > Thank you for your advice and consideration! >> > >> > Sincerely, >> > Anatoli Korkin>> E-mail to subscribers: CHEMISTRY#%#ccl.net or use:>> >> E-mail to administrators: CHEMISTRY-REQUEST#%#ccl.net or use>> >> >> -- Alan Shusterman Chemistry Department Reed College 3203 SE Woodstock Blvd Portland, OR 97202-8199 503-517-7699 http://blogs.reed.edu/alan/ "Patience, persistence, and a sense of humor." Dave Barrett (1956-2017, Reed College '77) --00000000000075ad8c05c46f8431 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
> ... Like a virtual lab. ... There are plenty mov= ies on youtube of any level of complexity but they would not provide a hands-on=20 experience and ability to change some parameters=C2=A0to get feeling of doi= ng a "chemistry experiment".

I understand = and endorse what you are saying. Being able to "play" with a mode= l (experiment) and see how the observables respond to adjustments in parame= ters and/or molecular composition/structure is exactly what Odyssey is desi= gned to do. Also, not only does it contain multiple experiments, mos= t of these experiments provide students with a set of compounds to investig= ate. Odyssey's presentation of the simulation is also much richer than = any movie is likely to be. There are a number of easy-to-use tools that tak= e the user more deeply into the visualizations, e.g., atom tools, tools for= focusing on particular sets of atoms, much more. And, beyond visuation its= elf, there are tools in the software for gathering/displaying numerical dat= a (graphs, charts) about the simulation.

Like I sa= id, Odyssey is not free. I've purchased a campus-wide site license in t= he past to make Odyssey available to all students on my campus. But I sugge= st you "try before you buy". Request a demo trial. You can then f= ollow the tutorials provided with the software, and whenever you're rea= dy, jump into the large number of models that are provided. And, like I sai= d, even if you don't go this route, I think you'll find a lot in Od= yssey that inspires you in whatever direction you go.

<= div>Good luck! Alan

On Thu, Jun 10, 2021 at 11:24 AM Anatoli Kork= in korkin.-#-.nanoandgiga.com <owner-chemistry-#-ccl.net> wrot= e:
I need something which students and teachers with no professional = chemistry background could use as demo lessons of "virtual chemistry&q= uot;. Like a virtual lab. The best analogy is chemistry demonstration in th= e class by mixing some liquids with a visual result: color change, gas or s= ediment, etc. In this case the visual effects would be conformation changes= or formation of a molecular cluster (temperature down) or cluster evaporat= ion (temperature up). There are plenty movies on youtube of any level of co= mplexity but they would not provide a hands-on experience and ability to ch= ange some parameters=C2=A0to get feeling of doing a "chemistry experim= ent".

Best regards,
Anatoli Kor= kin
Adjunct Professor
=
School of Molecular Sciences
Arizona State University<= /div>
Pr= esident of Nano and Giga Solutions Inc.



On = Wed, Jun 9, 2021 at 7:48 PM Elaine Meng meng{=3D}cgl.ucsf.edu <owner-chemistry#%#ccl.net> wrot= e:

Sent to CCL by: Elaine Meng [meng-$-cgl.ucsf.edu]
If this is for noncommercial use, you could take a look at the Sophia plugi= n to UCSF Chimera; both are free downloads for noncommercial purposes:

https://www.rbvi.ucsf.edu/chimera/plugi= ns/plugins.html#sophia
https://sophia-web.appspot.com/
https://www.rbvi.ucsf.edu/chimera/index.html

However, Sophia may be intended more to teach principles of MD using simple= systems, than to teach chemistry per se.=C2=A0 Also developed mainly for M= ac although documentation says most features also work on Windows, and whil= e it may be easy for you to install, not necessarily so for students.

Best,
Elaine
-----
Elaine C. Meng, Ph.D.=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco


> On Jun 9, 2021, at 7:05 AM, Anatoli Korkin korkin-x-nanoandgiga.= com <owner-chemistry~!~ccl.net> wrote:
>
>
> Sent to CCL by: "Anatoli=C2=A0 Korkin" [korkin^nanoandgiga.com<= /a>]
> I am looking for a free MM/MD program easy to install and operate in W= indows PC
> environment to design some chemistry lessons for high school students,= e.g.
> conformational changes and condensation/evaporation with temperature c= hange.
> Even better if someone, who is expert in MM/MD, would be interested to= join the
> project and develop some video lessons. See examples on my youtube cha= nnel
> "Atomic Scale Design for Newbies":
>
> https://www.youtube.com/channel/UCQZL1U= yyBo7HuN-FA286YWA
>
> Thank you for your advice and consideration!
>
> Sincerely,
> Anatoli Korkin



-=3D This is automatically added to each message by the mailing script =3D-=
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--
Alan Shusterman
Chemistry Department
Reed College
3203 SE Woodst= ock Blvd
Portland, OR 97202-8199
503-517-7699
http://blogs.reed.edu/alan/
&q= uot;Patience, persistence, and a sense of humor." Dave Barrett (1956-2= 017, Reed College '77)
--00000000000075ad8c05c46f8431-- From owner-chemistry@ccl.net Thu Jun 10 19:22:01 2021 From: "Thomas Manz tmanz|nmsu.edu" To: CCL Subject: CCL: MM/MD program for Windows PC Message-Id: <-54388-210610165133-17607-EyKEL0Uy92B9fDZaKfwoew_._server.ccl.net> X-Original-From: Thomas Manz Content-Type: multipart/alternative; boundary="000000000000c93ec505c46f8d3f" Date: Thu, 10 Jun 2021 14:51:12 -0600 MIME-Version: 1.0 Sent to CCL by: Thomas Manz [tmanz###nmsu.edu] --000000000000c93ec505c46f8d3f Content-Type: text/plain; charset="UTF-8" Hi Joe, Some of the Nanohub.org interactive modules/tools may be interesting to check out. These have a graphical user interface (GUI) where users can select computational parameters. The calculation is then run on a backend cluster at Nanohub, and the results are brought back into the GUI and displayed to the user. Everything is done through a web browser with no need to install software, and it runs in real time. The user does not need to supply any computational resources, because the Nanohub cluster runs the simulation. It is free to use. They have a lot of different kinds of modules/tools that relate to various aspects of nanochemistry. Sincerely, Thomas Manz, PhD Associate Professor tmanz:-:nmsu.edu http://wordpress.nmsu.edu/tmanz/ New Mexico State University Department of Chemical & Materials Engineering On Thu, Jun 10, 2021 at 2:40 PM Joseph Leonard jleonard42!A!gmail.com < owner-chemistry:-:ccl.net> wrote: > You might want to look at the educational offerings from Wavefunction ( > www.wavefun.com). They also wrote experimental books as I recall. > > Joe Leonard > > On Thu, Jun 10, 2021 at 2:04 PM Anatoli Korkin korkin.^.nanoandgiga.com < > owner-chemistry^ccl.net> wrote: > >> I need something which students and teachers with no professional >> chemistry background could use as demo lessons of "virtual chemistry". Like >> a virtual lab. The best analogy is chemistry demonstration in the class by >> mixing some liquids with a visual result: color change, gas or sediment, >> etc. In this case the visual effects would be conformation changes or >> formation of a molecular cluster (temperature down) or cluster evaporation >> (temperature up). There are plenty movies on youtube of any level of >> complexity but they would not provide a hands-on experience and ability to >> change some parameters to get feeling of doing a "chemistry experiment". >> >> Best regards, >> Anatoli Korkin >> Adjunct Professor >> School of Molecular Sciences >> Arizona State University >> webapp4.asu.edu/directory/person/1169125 >> President of Nano and Giga Solutions Inc. >> nanoandgiga.com/board/korkin.html >> >> >> >> On Wed, Jun 9, 2021 at 7:48 PM Elaine Meng meng{=}cgl.ucsf.edu < >> owner-chemistry#%#ccl.net> wrote: >> >>> >>> Sent to CCL by: Elaine Meng [meng-$-cgl.ucsf.edu] >>> If this is for noncommercial use, you could take a look at the Sophia >>> plugin to UCSF Chimera; both are free downloads for noncommercial purposes: >>> >>> https://www.rbvi.ucsf.edu/chimera/plugins/plugins.html#sophia >>> https://sophia-web.appspot.com/ >>> https://www.rbvi.ucsf.edu/chimera/index.html >>> >>> However, Sophia may be intended more to teach principles of MD using >>> simple systems, than to teach chemistry per se. Also developed mainly for >>> Mac although documentation says most features also work on Windows, and >>> while it may be easy for you to install, not necessarily so for students. >>> >>> Best, >>> Elaine >>> ----- >>> Elaine C. Meng, Ph.D. >>> UCSF Chimera(X) team >>> Department of Pharmaceutical Chemistry >>> University of California, San Francisco >>> >>> >>> > On Jun 9, 2021, at 7:05 AM, Anatoli Korkin korkin-x-nanoandgiga.com >>> wrote: >>> > >>> > >>> > Sent to CCL by: "Anatoli Korkin" [korkin^nanoandgiga.com] >>> > I am looking for a free MM/MD program easy to install and operate in >>> Windows PC >>> > environment to design some chemistry lessons for high school students, >>> e.g. >>> > conformational changes and condensation/evaporation with temperature >>> change. >>> > Even better if someone, who is expert in MM/MD, would be interested to >>> join the >>> > project and develop some video lessons. See examples on my youtube >>> channel >>> > "Atomic Scale Design for Newbies": >>> > >>> > https://www.youtube.com/channel/UCQZL1UyyBo7HuN-FA286YWA >>> > >>> > Thank you for your advice and consideration! >>> > >>> > Sincerely, >>> > Anatoli Korkin>>> E-mail to subscribers: CHEMISTRY#%#ccl.net or use:>>> >>> E-mail to administrators: CHEMISTRY-REQUEST#%#ccl.net or use>>> >>> >>> -- > -- > "Peter Thiel was right, we just can't build cool sh*t anymore. I really > did want a flying car, and all I have is 140 characters and promises of AI > that never come true." > --000000000000c93ec505c46f8d3f Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Hi Joe,

Some of the Nanohub.org in= teractive modules/tools may be interesting to check out. These have a graph= ical user interface (GUI) where users can select computational parameters. = The calculation is then run on a backend cluster at Nanohub, and the result= s are brought back into the GUI and displayed to the user. Everything is do= ne through a web browser with no need to install software, and it runs in r= eal time. The user does not need to supply any computational=C2=A0resources= , because the Nanohub cluster runs the simulation. It is free to use. They = have a lot of different kinds of modules/tools that relate to various aspec= ts of nanochemistry.

Sincerely,

Thomas Manz, PhD

Associate Professor

tmanz:-:nms= u.edu

http://wordpress.n= msu.edu/tmanz/

New Mexico State University

Department of Chemical & Materials=C2=A0Engineering


On Thu, Jun 10, 2021 at 2:40 PM Joseph = Leonard jleonard42!A!gmail.com <owner-chemistry:-:ccl.net> wrote:<= br>
You might want to look at the educational offerings from Wavefunction (www.wavefun.com).=C2= =A0 They also wrote experimental books as I recall.
=
Joe Leonard=C2=A0

On Thu, Jun 10, 2021 at 2= :04 PM Anatoli Korkin korkin.^.nanoandgiga.com <owner-chemistry^ccl.net> wrote:
I need so= mething which students and teachers with no professional chemistry backgrou= nd could use as demo lessons of "virtual chemistry". Like a virtu= al lab. The best analogy is chemistry demonstration in the class by mixing = some liquids with a visual result: color change, gas or sediment, etc. In t= his case the visual effects would be conformation changes or formation of a= molecular cluster (temperature down) or cluster evaporation (temperature u= p). There are plenty movies on youtube of any level of complexity but they = would not provide a hands-on experience and ability to change some paramete= rs=C2=A0to get feeling of doing a "chemistry experiment".
Best regards,
Anatoli Korkin
Adjunct Professor
School= of Molecular Sciences
Arizona State University
President of Nano a= nd Giga Solutions Inc.



On Wed, Jun 9, 2021 = at 7:48 PM Elaine Meng meng{=3D}cgl.ucsf.edu <owner-chemistry#%#ccl.net> wrote:

Sent to CCL by: Elaine Meng [meng-$-cgl.ucsf.edu]
If this is for noncommercial use, you could take a look at the Sophia plugi= n to UCSF Chimera; both are free downloads for noncommercial purposes:

https://www.rbvi.ucsf.edu/chimera/plugi= ns/plugins.html#sophia
https://sophia-web.appspot.com/
https://www.rbvi.ucsf.edu/chimera/index.html

However, Sophia may be intended more to teach principles of MD using simple= systems, than to teach chemistry per se.=C2=A0 Also developed mainly for M= ac although documentation says most features also work on Windows, and whil= e it may be easy for you to install, not necessarily so for students.

Best,
Elaine
-----
Elaine C. Meng, Ph.D.=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco


> On Jun 9, 2021, at 7:05 AM, Anatoli Korkin korkin-x-nanoandgiga.= com <owner-chemistry~!~ccl.net> wrote:
>
>
> Sent to CCL by: "Anatoli=C2=A0 Korkin" [korkin^nanoandgiga.com<= /a>]
> I am looking for a free MM/MD program easy to install and operate in W= indows PC
> environment to design some chemistry lessons for high school students,= e.g.
> conformational changes and condensation/evaporation with temperature c= hange.
> Even better if someone, who is expert in MM/MD, would be interested to= join the
> project and develop some video lessons. See examples on my youtube cha= nnel
> "Atomic Scale Design for Newbies":
>
> https://www.youtube.com/channel/UCQZL1U= yyBo7HuN-FA286YWA
>
> Thank you for your advice and consideration!
>
> Sincerely,
> Anatoli Korkin



-=3D This is automatically added to each message by the mailing script =3D-=
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--
--
"Peter Thiel was right, we just can't build cool sh*t anymore. = I really did want a flying car, and all I have is 140 characters and promis= es of AI that never come true."
--000000000000c93ec505c46f8d3f-- From owner-chemistry@ccl.net Thu Jun 10 19:57:00 2021 From: "Laurence Cuffe cuffe++mac.com" To: CCL Subject: CCL: QM codes NOT written in Fortran Message-Id: <-54389-210610172540-7497-pQ5qXSVebfTu2P7KCHQRcw\a/server.ccl.net> X-Original-From: Laurence Cuffe Content-Type: multipart/alternative; boundary="Apple-Mail=_D55C6B92-1FD1-4427-8B13-D6584EB66660" Date: Thu, 10 Jun 2021 22:25:25 +0100 Mime-Version: 1.0 (Mac OS X Mail 11.5 \(3445.9.7\)) Sent to CCL by: Laurence Cuffe [cuffe#mac.com] --Apple-Mail=_D55C6B92-1FD1-4427-8B13-D6584EB66660 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=utf-8 I Started coding some time back, in Fortran IV. At that time Fortran was = the luxury, and Machine code was for the real Nerds. At a later point, i = spent a significant amount of time programming in C. My recent encounters with programming have included Python, Java, = Javascript, and Kotlin. Each of them address specific problems.=20 I=E2=80=99ve seen the problems of maintaining and testing a large code = base in Fortran. It can be very scientist friendly, and compilers can be = very optimised. However the code does not scale well to really big = projects with a lot of complexity. This is a problem which language designers have been working on, with = greater or lesser success, for many years. Modern languages make larger = projects more manageable, and what you loose out on in faster compute = cycles, is compensated for in the time lost spent debugging, testing and = just getting the code to run.=20 The kind of solution mentioned below, C++ with a Python front end, is = generally an effective comprimise. My 2c. Laurence Cuffe > On 10 Jun 2021, at 17:02, T. Daniel Crawford crawdad%a%vt.edu = > wrote: >=20 > Psi4 (psicode.org ) is C++ with a Python front = end. >=20 > -TDC > -- > Prof. T. Daniel Crawford > crawdad . vt.edu >=20 >> On Jun 10, 2021, at 12:39 AM, Neese, Frank neese-*-kofo.mpg.de = > wrote: >>=20 >> ORCA is entirely written in C++. AFAIK, MPQC too.=20 >>=20 >>=20 >> Sent from my iPad >>=20 >>> On 10. Jun 2021, at 03:14, Joe Leonard jleonard42%x%gmail.com = > wrote: >>>=20 >>> =EF=BB=BF Folks, are there QM packages that have managed to = =E2=80=9Close=E2=80=9D all their fortran code or are new enough to have = been developed in a different language or different languages? I have = not seen good comments re: the Mac M1 chipset and I=E2=80=99m curious = whether there are alternatives=E2=80=A6 >>>=20 >>> I=E2=80=99m sure others would be interested as well. >>>=20 >>> Joe Leonard >>> =E2=80=94 >>> "Peter Thiel was right, we just can't build cool sh*t anymore. I = really did want a flying car, and all I have is 140 characters and = promises of AI that never come true." >>>=20 >=20 --Apple-Mail=_D55C6B92-1FD1-4427-8B13-D6584EB66660 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=utf-8
I Started coding some = time back, in Fortran IV. At that time Fortran was the luxury, and = Machine code was for the real Nerds. At a later point, i spent a = significant amount of time programming in C.
My recent = encounters with programming have included Python, Java, Javascript, and = Kotlin. Each of them address specific problems. 
I=E2=80=99ve seen the problems of maintaining and testing a = large code base in Fortran. It can be very scientist friendly, and = compilers can be very optimised. However the code does not scale well to = really big projects with a lot of complexity.
This = is a problem which language designers have been working on, with greater = or lesser success, for many years. Modern languages make larger projects = more manageable, and what you loose out on in faster compute cycles, is = compensated for in the time lost spent debugging, testing and just = getting the code to run. 
The kind of solution = mentioned below, C++ with a Python front end, is generally an effective = comprimise.
My 2c.
Laurence = Cuffe

On 10 Jun 2021, at 17:02, T. = Daniel Crawford crawdad%a%vt.edu= <owner-chemistry###ccl.net> wrote:

Psi4 (psicode.org) is C++ with a = Python front end.

-TDC
--
Prof. T. Daniel Crawford
crawdad . vt.edu

On Jun 10, 2021, at 12:39 AM, Neese, Frank neese-*-kofo.mpg.de <owner-chemistry . = ccl.net> wrote:

ORCA is entirely written in C++. AFAIK, MPQC too. 


Sent from my iPad

On 10. Jun 2021, at 03:14, Joe = Leonard jleonard42%x%gmail.com <owner-chemistry . ccl.net> wrote:

=EF=BB=BF Folks, are there QM packages that = have managed to =E2=80=9Close=E2=80=9D all their fortran code or are new = enough to have been developed in a different language or different = languages?  I have not seen good comments re: the Mac M1 chipset = and I=E2=80=99m curious whether there are alternatives=E2=80=A6

I=E2=80=99m sure others would be interested as = well.

Joe Leonard
=E2=80=94
"Peter Thiel was right, we just can't build cool sh*t anymore. I = really did want a flying car, and all I have is 140 characters = and promises of AI that never come true."



= --Apple-Mail=_D55C6B92-1FD1-4427-8B13-D6584EB66660-- From owner-chemistry@ccl.net Thu Jun 10 20:32:00 2021 From: "Piotr Gauden gaudi*umk.pl" To: CCL Subject: CCL: MM/MD program for Windows PC Message-Id: <-54390-210610181206-6868-NOLTPNxHAmJVfky3lMKA9g!^!server.ccl.net> X-Original-From: Piotr Gauden Content-Disposition: inline Content-Type: text/plain; charset=utf-8; format=flowed; DelSp=Yes Date: Fri, 11 Jun 2021 00:11:53 +0200 MIME-Version: 1.0 Sent to CCL by: Piotr Gauden [gaudi[#]umk.pl] Dear Anatoli, I recommend applet. https://physics.weber.edu/schroeder/md/InteractiveMD.html You can also collect numerical values for the different virtual experiments. Best regards, Piotr Cytowanie "Brian Skinn brian.skinn : gmail.com" : > Anatoli, > > I did a quick Google search for "interactive molecular model of > condensation", and discovered this: http://mw.concord.org/nextgen/ > > I have no experience with them at all, and cannot make any particular > recommendation. The demonstration on the landing page seems exactly like > what you describe, though. I'm not sure how you would go about making use > of their product...it might involve becoming one of their "partners"? > > > Good luck, > Brian > > On Thu, Jun 10, 2021 at 3:30 PM Anatoli Korkin korkin.{=}.nanoandgiga.com < > owner-chemistry{=}ccl.net> wrote: > >> I need something which students and teachers with no professional >> chemistry background could use as demo lessons of "virtual chemistry". Like >> a virtual lab. The best analogy is chemistry demonstration in the class by >> mixing some liquids with a visual result: color change, gas or sediment, >> etc. In this case the visual effects would be conformation changes or >> formation of a molecular cluster (temperature down) or cluster evaporation >> (temperature up). There are plenty movies on youtube of any level of >> complexity but they would not provide a hands-on experience and ability to >> change some parameters to get feeling of doing a "chemistry experiment". >> >> Best regards, >> Anatoli Korkin >> Adjunct Professor >> School of Molecular Sciences >> Arizona State University >> webapp4.asu.edu/directory/person/1169125 >> President of Nano and Giga Solutions Inc. >> nanoandgiga.com/board/korkin.html >> >> >> >> On Wed, Jun 9, 2021 at 7:48 PM Elaine Meng meng{=}cgl.ucsf.edu < >> owner-chemistry#%#ccl.net> wrote: >> >>> >>> Sent to CCL by: Elaine Meng [meng-$-cgl.ucsf.edu] >>> If this is for noncommercial use, you could take a look at the Sophia >>> plugin to UCSF Chimera; both are free downloads for noncommercial purposes: >>> >>> https://www.rbvi.ucsf.edu/chimera/plugins/plugins.html#sophia >>> https://sophia-web.appspot.com/ >>> https://www.rbvi.ucsf.edu/chimera/index.html >>> >>> However, Sophia may be intended more to teach principles of MD using >>> simple systems, than to teach chemistry per se. Also developed mainly for >>> Mac although documentation says most features also work on Windows, and >>> while it may be easy for you to install, not necessarily so for students. >>> >>> Best, >>> Elaine >>> ----- >>> Elaine C. Meng, Ph.D. >>> UCSF Chimera(X) team >>> Department of Pharmaceutical Chemistry >>> University of California, San Francisco >>> >>> >>> > On Jun 9, 2021, at 7:05 AM, Anatoli Korkin korkin-x-nanoandgiga.com >>> wrote: >>> > >>> > >>> > Sent to CCL by: "Anatoli Korkin" [korkin^nanoandgiga.com] >>> > I am looking for a free MM/MD program easy to install and operate in >>> Windows PC >>> > environment to design some chemistry lessons for high school students, >>> e.g. >>> > conformational changes and condensation/evaporation with temperature >>> change. >>> > Even better if someone, who is expert in MM/MD, would be interested to >>> join the >>> > project and develop some video lessons. See examples on my youtube >>> channel >>> > "Atomic Scale Design for Newbies": >>> > >>> > https://www.youtube.com/channel/UCQZL1UyyBo7HuN-FA286YWA >>> > >>> > Thank you for your advice and consideration! >>> > >>> > Sincerely, >>> > Anatoli Korkin>> E-mail to subscribers: CHEMISTRY#%#ccl.net or use:>> >>> E-mail to administrators: CHEMISTRY-REQUEST#%#ccl.net or use>> >>> >>> ------------------------------------------------------------------------------------------- ------------------------------------------------------------------------------------------- dr hab. Piotr A. Gauden, prof. UMK gaudi+/-uni.torun.pl Nicholas Copernicus University, Chair of Materials Chemistry, Adsorption and Catalysis Carbon Materials Application in Electrochemistry and Environmental Protection Reserch Group 87-100 Torun Gagarin St. 7 Tel. (+48) (056) 611-45-12 Fax. (+48) (056) 654-24-77 ORCID: https://orcid.org/0000-0002-0474-3771 Webpage: https://www.researchgate.net/profile/Piotr_Gauden GoogleScholar: https://scholar.google.pl/citations?user=BB4IueMAAAAJ&hl=pl ------------------------------------------------------------------------------------------- ------------------------------------------------------------------------------------------- From owner-chemistry@ccl.net Thu Jun 10 21:06:00 2021 From: "Phil Hasnip phil.hasnip]_[york.ac.uk" To: CCL Subject: CCL: QM codes NOT written in Fortran Message-Id: <-54391-210610200247-17107-7a5ueLdfayOOfFfqrdYsqA%x%server.ccl.net> X-Original-From: Phil Hasnip Content-Type: multipart/alternative; boundary="000000000000c802ad05c4723953" Date: Fri, 11 Jun 2021 01:02:27 +0100 MIME-Version: 1.0 Sent to CCL by: Phil Hasnip [phil.hasnip:_:york.ac.uk] --000000000000c802ad05c4723953 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable Dear Joe, The GNU toolchain works fine (at least gfortran 11) on Mac M1, and we've certainly used it to compile and run CASTEP successfully (www.castep.org). Obviously you need to make sure you also have the correct libraries, e.g. OpenBLAS, FFTW, but MacPorts should take care of that. We generally find gfortran performance to be very competitive, and of course it's value for money is excellent! Having said that, the NAG compiler is fantastic for developing software, but not for performance (that's not a criticism, that's a deliberate design decision by NAG). All the best, Phil ---------------------------------------------------------------------------= --------- Dr Phil Hasnip Email: phil.hasnip^york.ac.uk EPSRC RSE Fellow Web: www-users.york.ac.uk/~pjh503 Dept of Physics University of York Tel: +44 (0)1904 322225 York YO10 5DD Virus-free. www.avast.com <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2> On Thu, 10 Jun 2021 at 05:10, Joe Leonard jleonard42{}gmail.com < owner-chemistry^ccl.net> wrote: > > On Jun 9, 2021, at 10:07 PM, Phil Hasnip phil.hasnip[-]york.ac.uk < > owner-chemistry__ccl.net> wrote: > > I'm confused about your Mac M1 chipset reference; how does this relate to > your Fortran question? There are good ARM Fortran compilers, if that's wh= at > you're worried about. > > > Phil, what compilers are up and working on the MacOS/M1 combination? I a= m > aware of the NAG compiler, which has issues for commercial development > (licensing) so I have been told. Also, given the staggeringly greater > interest in C/C++ on all sorts of machines, I would think that portabilit= y > would suggest alternate languages for new work - Python is a great > control-level language, but as you mentioned you need math underneath. > > Joe > =E2=80=94 > "Peter Thiel was right, we just can't build cool sh*t anymore. I really > did want a flying car, and all I have is 140 characters and promises of A= I > that never come true." > > --000000000000c802ad05c4723953 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Dear Joe,

The GNU toolchain works fine = (at least gfortran 11) on Mac M1, and we've certainly used it to compil= e and run CASTEP successfully (www.castep.org). Obviously you need to make sure you also have = the correct libraries, e.g. OpenBLAS, FFTW, but MacPorts should take care o= f that.

We generally=C2=A0find gfortran performanc= e to be very competitive, and of course it's value for money is excelle= nt! Having said that, the NAG compiler is fantastic for developing software= , but not for performance (that's not a criticism, that's a deliber= ate design decision by NAG).

All the best,

Phil

----------------------= --------------------------------------------------------------
Dr Phil H= asnip =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0 Email: phil= .hasnip^york.ac.uk
EPSRC RSE Fellow=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0 Web:=C2=A0 www-users.york.ac.uk/~pjh503
Dept of Physics
Un= iversity of York =C2=A0 =C2=A0 =C2=A0 =C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 Tel: = =C2=A0=C2=A0=C2=A0 +44 (0)1904 322225
York YO10 5DD


3D"" Virus-free. www.avast.com

On Thu, 10 Jun 2021 at 05:10, Joe Leonard jleonard42{}gmail.com <owner-chemistry^ccl.net>= wrote:
On Jun 9, 2021, at 10:07 PM, Phil Hasn= ip phil.hasnip[-]york.ac.uk= <owne= r-chemistry__ccl.net> wrote:

I'm confused about your Mac M1 chipset reference= ; how does this relate to your Fortran question? There are good ARM Fortran= compilers, if that's what you're worried about.=C2=A0
=

Phil, what compilers are up and working o= n the MacOS/M1 combination?=C2=A0 I am aware of the NAG compiler, which has= issues for commercial development (licensing) so I have been told.=C2=A0 A= lso, given the staggeringly greater interest in C/C++ on all sorts of machi= nes, I would think that portability would suggest alternate languages for n= ew work - Python is a great control-level language, but as you mentioned yo= u need math underneath.

Joe
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