From owner-chemistry@ccl.net Fri Jun 11 09:07:01 2021 From: "Joseph Leonard jleonard42||gmail.com" To: CCL Subject: CCL: QM codes NOT written in Fortran Message-Id: <-54392-210610230708-30154-xo11xK75a4TCOTV3/d7q7A(~)server.ccl.net> X-Original-From: Joseph Leonard Content-Type: multipart/alternative; boundary="000000000000327a9305c474cd52" Date: Thu, 10 Jun 2021 23:06:50 -0400 MIME-Version: 1.0 Sent to CCL by: Joseph Leonard [jleonard42^gmail.com] --000000000000327a9305c474cd52 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable Phil, glad to hear that you had success with gfortran on that platform. It=E2=80=99s been a long time sopince I worked in fortran and those doing i= t more recently had a very dim view of that suite. I will pass it along. Joe On Thu, Jun 10, 2021 at 10:36 PM Phil Hasnip phil.hasnip]_[york.ac.uk < owner-chemistry^ccl.net> wrote: > 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 > > <#m_-4984180958677803491_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 t= o >> your Fortran question? There are good ARM Fortran compilers, if that's w= hat >> you're worried about. >> >> >> Phil, what compilers are up and working on the MacOS/M1 combination? I >> am aware of the NAG compiler, which has issues for commercial developmen= t >> (licensing) so I have been told. Also, given the staggeringly greater >> interest in C/C++ on all sorts of machines, I would think that portabili= ty >> 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 = AI >> that never come true." >> >> -- -- "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." --000000000000327a9305c474cd52 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Phil, glad to hear that you had success with gfortran on = that platform. It=E2=80=99s been a long time sopince I worked in fortran an= d those doing it more recently had a very dim view of that suite.=C2=A0 I w= ill pass it along.=C2=A0

Joe

On Thu, Jun 10, 2021 at 10:36 PM Phil Hasnip phil.hasnip]_[york.ac.uk <owner-chemistry^ccl.net> wrote:
Dear Joe,

The GNU toolcha= in works fine (at least gfortran 11) on Mac M1, and we've certainly use= d 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 shou= ld take care of that.

We generally=C2=A0find gfort= ran performance to be very competitive, and of course it's value for mo= ney is excellent! Having said that, the NAG compiler is fantastic for devel= oping software, but not for performance (that's not a criticism, that&#= 39;s a deliberate design decision by NAG).

All the b= est,

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
= 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=


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

On Thu, 10 Jun 2021 at 05:10, Jo= e Leonard jleonard42{}gmail.= com <owner-chemistry##ccl.net> wrote:

On Ju= n 9, 2021, at 10:07 PM, Phil Hasnip phil.hasnip[-]york.ac.uk <owner-chemistry__ccl.net> wrote:
<= br>
I'm confused ab= out your Mac M1 chipset reference; how does this relate to your Fortran que= stion? There are good ARM Fortran compilers, if that's what you're = worried about.=C2=A0

Phil, wh= at compilers are up and working on the MacOS/M1 combination?=C2=A0 I am awa= re of the NAG compiler, which has issues for commercial development (licens= ing) so I have been told.=C2=A0 Also, given the staggeringly greater intere= st in C/C++ on all sorts of machines, I would think that portability would = suggest alternate languages for new work - Python is a great control-level = language, but as you mentioned you need math underneath.

Joe
<= div style=3D"text-align:start;text-indent:0px">
<= div style=3D"text-align:start;text-indent:0px">
=E2=80=94
<= div dir=3D"auto" style=3D"text-align:start;text-indent:0px">
<= div style=3D"text-align:start;text-indent:0px">
<= div style=3D"text-align:start;text-indent:0px">
"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 hav= e is 140=C2=A0characters and promises of AI that never=C2=A0come true."= ;
<= /div>
<= /div>
<= /div>
<= /div>
<= /div>

--
--
"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."
--000000000000327a9305c474cd52-- From owner-chemistry@ccl.net Fri Jun 11 13:01:00 2021 From: "Marcos Verissimo Alves marcos_verissimo+/-id.uff.br" To: CCL Subject: CCL: QM codes NOT written in Fortran Message-Id: <-54393-210611113237-31536-HJYa5pDBDK7hI7zDaoB8aA-.-server.ccl.net> X-Original-From: Marcos Verissimo Alves Content-Type: multipart/alternative; boundary="000000000000323fd905c47f3747" Date: Fri, 11 Jun 2021 12:31:53 -0300 MIME-Version: 1.0 Sent to CCL by: Marcos Verissimo Alves [marcos_verissimo,,id.uff.br] --000000000000323fd905c47f3747 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable Hi everyone, Also, remember that there is a free version of the PGI compiler with CUDA, the PGI Community Edition: https://developer.nvidia.com/openacc-toolkit I'm not too sure about its efficiency, but I suppose it would be comparable to GCC, which is very good indeed. If you need to compile or develop a GPU-accelerated code for NVIDIA GPUs, it's certainly something to try out. Best, Marcos --- Prof. Dr. Marcos Verissimo Alves Prof. Adjunto II, Curso de F=C3=ADsica Computacional Instituto de Ci=C3=AAncias Exatas Universidade Federal Fluminense Volta Redonda - RJ, Brasil Em sex., 11 de jun. de 2021 =C3=A0s 12:08, Joseph Leonard jleonard42||gmail= .com < owner-chemistry:ccl.net> escreveu: > Phil, glad to hear that you had success with gfortran on that platform. > It=E2=80=99s been a long time sopince I worked in fortran and those doing= it more > recently had a very dim view of that suite. I will pass it along. > > Joe > > On Thu, Jun 10, 2021 at 10:36 PM Phil Hasnip phil.hasnip]_[york.ac.uk < > owner-chemistry%%ccl.net > wrote: > >> 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 >> >> <#m_4969243596422521063_m_-4984180958677803491_DAB4FAD8-2DD7-40BB-A1B8-4= E2AA1F9FDF2> >> >> 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 >>> what you're worried about. >>> >>> >>> Phil, what compilers are up and working on the MacOS/M1 combination? I >>> am aware of the NAG compiler, which has issues for commercial developme= nt >>> (licensing) so I have been told. Also, given the staggeringly greater >>> interest in C/C++ on all sorts of machines, I would think that portabil= ity >>> 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= AI >>> that never come true." >>> >>> -- > -- > "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." > --000000000000323fd905c47f3747 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Hi everyone,

Also, remember that = there is a free version of the PGI compiler with CUDA, the PGI Community Ed= ition:=C2=A0https:= //developer.nvidia.com/openacc-toolkit

I'm not t= oo sure about its efficiency, but I suppose it would be comparable to GCC, = which is very good indeed. If you need to compile or develop a GPU-accelera= ted code for NVIDIA GPUs, it's certainly something to try out.

Best,

Marcos=C2=A0

---

Prof. Dr.= Marcos Verissimo Alves
Prof. Adjunto II, Curso de F=C3=ADsica Computac= ional
Instituto de Ci=C3=AAncias= Exatas
Universidade Federal Fluminense
Volt= a Redonda - RJ, Brasil
<= /div>

Em sex., 11 de jun. de 2021 =C3=A0s 12:08, Joseph Leonard j= leonard42||gmail.com <owner-chemistry:ccl.net> escreveu:
Phil,= glad to hear that you had success with gfortran on that platform. It=E2=80= =99s been a long time sopince I worked in fortran and those doing it more r= ecently had a very dim view of that suite.=C2=A0 I will pass it along.=C2= =A0

Joe

On Thu, Jun = 10, 2021 at 10:36 PM Phil Hasnip phil.hasnip]_[york.ac.uk <owner-chemistry%%ccl.net> wrote:
Dear J= oe,

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

<= /div>

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 Hasnip phil.hasnip[-]york.ac.uk <owner-chemistry__ccl.net= > wrote:

I'm confused about your Mac M1 chipset reference; how does this rela= te to your Fortran question? There are good ARM Fortran compilers, if that&= #39;s what you're worried about.=C2=A0
<= div>
Phil, what compilers are up and working on the MacOS/M1 combi= nation?=C2=A0 I am aware of the NAG compiler, which has issues for commerci= al development (licensing) so I have been told.=C2=A0 Also, given the stagg= eringly greater interest in C/C++ on all sorts of machines, I would think t= hat portability would suggest alternate languages for new work - Python is = a great control-level language, but as you mentioned you need math undernea= th.

Joe
<= div style=3D"text-align:start;text-indent:0px">
<= div style=3D"text-align:start;text-indent:0px">
=E2=80=94
<= div dir=3D"auto" style=3D"text-align:start;text-indent:0px">
<= div style=3D"text-align:start;text-indent:0px">
<= div style=3D"text-align:start;text-indent:0px">
"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 hav= e is 140=C2=A0characters and promises of AI that never=C2=A0come true."= ;
<= /div>
<= /div>
<= /div>
<= /div>
<= /div>

--
--
"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."
--000000000000323fd905c47f3747-- From owner-chemistry@ccl.net Fri Jun 11 15:42:00 2021 From: "Anatoli Korkin korkin*_*nanoandgiga.com" To: CCL Subject: CCL: MM/MD program for Windows PC Message-Id: <-54394-210611153936-28703-V9PMNUAYsk2lSPym5LBPtQ%server.ccl.net> X-Original-From: Anatoli Korkin Content-Type: multipart/alternative; boundary="0000000000008d522e05c482aa61" Date: Fri, 11 Jun 2021 14:39:18 -0500 MIME-Version: 1.0 Sent to CCL by: Anatoli Korkin [korkin!^!nanoandgiga.com] --0000000000008d522e05c482aa61 Content-Type: text/plain; charset="UTF-8" Thank you very much, Brian! Next-Generation Molecular Workbench is really useful instrument for simple illustration of physics, chemistry and biology and I added in a collection of the lessons on my youtube channel: https://www.youtube.com/watch?v=pavnxcgKGhg I also installed LAMMPS executables on my Windows PC but may take some times for me to learn it myself and to generate a (relatively) simple algorithm of generating some lessons which high school students or at least teachers can use. If someone who reads this message is LAMMPS experts and is willing to help, it would be great! Best regards, Anatoli Korkin Tel: +1-480-329-5710 (WhatsApp, Viber, Telegram and WeChat); Skype: anatolik51 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 Thu, Jun 10, 2021 at 5:59 PM Brian Skinn brian.skinn : gmail.com < owner-chemistry_-_ccl.net> wrote: > 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>>> >>> >>> --0000000000008d522e05c482aa61 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Thank you very much, Brian!

Next-Generation Molecular Workbench is really useful instr= ument for simple illustration of physics, chemistry and biology and I added= in a collection of the lessons on my youtube=C2=A0channel:

<= /div>

I a= lso installed LAMMPS executables on my Windows PC but may take some times f= or me to learn it myself=C2=A0and to generate a (relatively) simple algorit= hm of generating some lessons which high school students or at least teache= rs can use. If someone who reads this message is LAMMPS experts and is will= ing to help, it would be great!=C2=A0=C2=A0

=
Best regard= s,
Anatoli Korkin
Tel: +1-48= 0-329-5710 (WhatsApp, Viber, Telegram and WeChat); =C2=A0Skype: anatolik51
Adjunct Professor
School of Molecular S= ciences
Arizona State University
President of Nano and Giga Solutio= ns Inc.

=


On Thu, Jun 10, 2021 at 5:59 PM Bri= an Skinn brian.skinn : gmail.com <owner-chemistry_-_ccl.net> wrote= :
Anatoli,

I did a quick Google search for "intera= ctive molecular model of condensation", and discovered this:=C2=A0http://mw.concord.= org/nextgen/

I have no experience with them at= all, and cannot make any particular recommendation. The demonstration on t= he landing page seems exactly like what you describe, though. I'm not s= ure how you would go about making use of their product...it might involve b= ecoming=C2=A0one of their "partners"?

Good luck,
Brian

On Thu, Jun 10, 2021 at 3:30 P= M 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-=
E-mail to subscribers: CHEMISTRY#%#ccl.net or use:
=C2=A0 =C2=A0 =C2=A0 http://www.ccl.net/cgi-bin/ccl/s= end_ccl_message

E-mail to administrators: CHEMISTRY-REQUEST#%#ccl.net or use
=C2=A0 =C2=A0 =C2=A0 http://www.ccl.net/cgi-bin/ccl/s= end_ccl_message
=C2=A0 =C2=A0 =C2=A0 http://www.ccl.net/chemistry/sub_un= sub.shtml

Before posting, check wait time at: http://www.ccl.net

Job: http://www.ccl.net/jobs
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/


--0000000000008d522e05c482aa61-- From owner-chemistry@ccl.net Fri Jun 11 17:46:00 2021 From: "Anatoli Korkin korkin:_:nanoandgiga.com" To: CCL Subject: CCL:G: MM/MD program for Windows PC Message-Id: <-54395-210611155146-1221-Iyi+cgOogcQXzvFwC4Ip5Q++server.ccl.net> X-Original-From: Anatoli Korkin Content-Type: multipart/alternative; boundary="000000000000e7943405c482d573" Date: Fri, 11 Jun 2021 14:51:26 -0500 MIME-Version: 1.0 Sent to CCL by: Anatoli Korkin [korkin ~ nanoandgiga.com] --000000000000e7943405c482d573 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable Hi Derek, Avogadro is a good free molecular builder and I used it in some of my lessons in combination with ArgusLab which is also free it provides same set of instruments as commercial programs such as Hyperchem. Both Avoagdro and ArgusLab are easy to learn and operate (see example in my series of lessons): https://www.youtube.com/channel/UCQZL1UyyBo7HuN-FA286YWA Per your advice I installed LAMMPS executables on my Windows PC but this is not a plug-and-play program. I will need time to learn it myself in order to generate some example and simple algorithms for students and school teachers. I wonder if someone from CCL folks who is familiar with LAMMPS might be interested to help either with some tutorials for me or by making a guest lesson in my channel. Best regards, Anatoli Korkin Tel: +1-480-329-5710 (WhatsApp, Viber, Telegram and WeChat); Skype: anatolik51 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 Chairman of the American-Russian Chamber of Commerce of Minnesota www.arccom.org On Thu, Jun 10, 2021 at 2:11 PM Derek Cashman derek.cashman-.-gmail.com < owner-chemistry[a]ccl.net> wrote: > 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 ther= e > 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 >> > > --000000000000e7943405c482d573 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Hi Derek,

A= vogadro is a good free molecular builder and I used it in some of my lesson= s in combination with ArgusLab=C2=A0 which is also free it provides same se= t of instruments as commercial programs such as Hyperchem. Both Avoagdro=C2= =A0and ArgusLab are easy to learn and operate (see example in my series=C2= =A0of lessons):


Per your advice I install= ed LAMMPS executables on my Windows PC but this is not a plug-and-play prog= ram. I will need time to learn it myself in order to generate some example = and simple algorithms=C2=A0 for students and school teachers. I wonder=C2= =A0if someone from CCL folks who is familiar with LAMMPS might be intereste= d to help either with some tutorials for me or by making a guest lesson in = my channel.=C2=A0

Best regards,
Anatoli Korkin
Tel: +1-480-329-5710 (WhatsApp, Vi= ber, Telegram and WeChat); =C2=A0Sk= ype: anatolik51
Adjunct P= rofessor
School of Molecular Sciences
Arizon= a State University
Chairman of the American-Russian Cham= ber of Commerce of Minnesota


On Thu, Jun 10, 2021 at 2:11 PM Derek Cashman derek.cas= hman-.-gmail.com <owner-chemistry[a]ccl.net> wrote:
Avogadro is an excellent and free software for modeling sm= all molecules. It includes several molecular mechanics force fields, and al= so has interfaces for Gaussian, NWChem, and GAMESS for quantum mechanical c= alculations as well. I have not used it for molecular dynamics, but there i= s an interface to LAMPPS that might be worth investigating as well.

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



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

"A drug is an= y substance which, when injected into a rat, produces a publishable, scient= ific paper.=E2=80=9D

On Wed, Jun 9, 2021 at 9:06 AM Anat= oli Korkin k= orkin-x-nanoandgiga.com <owner-chemistry%ccl.net> wrote:

Sent to CCL by: "Anatoli=C2=A0 Korkin" [korkin^nanoandgiga.com]=
I am looking for a free MM/MD program easy to install and operate in Window= s 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/UCQZL1UyyBo7= HuN-FA286YWA

Thank you for your advice and consideration!

Sincerely,
Anatoli Korkin

--000000000000e7943405c482d573--