From owner-chemistry@ccl.net Fri Jan 20 09:18:00 2012 From: "qiancheng shen qianchengshen%%gmail.com" To: CCL Subject: CCL: Chemical Drawing Programs review Message-Id: <-46172-120120085104-5114-d1pT6wPlW1fuAMkkHpDuiQ!A!server.ccl.net> X-Original-From: qiancheng shen Content-Type: multipart/alternative; boundary=00151750e2d44b46b904b6f5f8cb Date: Fri, 20 Jan 2012 21:50:55 +0800 MIME-Version: 1.0 Sent to CCL by: qiancheng shen [qianchengshen(0)gmail.com] --00151750e2d44b46b904b6f5f8cb Content-Type: text/plain; charset=windows-1252 Content-Transfer-Encoding: quoted-printable Dear Tamas, I tried the "Xemistry Web Sketcher", but the click response is too slow. I selected the button "single bond" and clicked on the draw area,then it cost several seconds to generate bond on the screen. I guess it may fetch something from the server instead of generating them by the client itself. Also, it made my IE explore crashed two times!! I have to say "ChemWriter" is much better, since it is fast and work well even on the IE6 explore. Sorry for my terrible english. Qiancheng 2012/1/19 Wolf Ihlenfeldt wdi/axemistry.com > > Strangely, this review is completely missing the technologically unique > Web sketcher originally developed for PubChem and accessible in an enhanc= ed > version at www.xemistry.com/edit/frame.html > > This tool is the only full-featured Web structure editor which is *not* a > plug-in (with all its platform and installation issues) nor a Java applet > (with its own JVM engine presence and versioning problems, plus download > time issues). Compared to other Web editors of any kind, it can access a > much broader range of Internet structure databases directly (over 2 dozen > currently), and it supports a much larger list of I/O formats (for exampl= e, > it supports SDF3000 and original ChemDraw CDX/CDXML or ISISDraw skc/tgf > files as well as direct input and decoding of SMILES, SLN, JME strings, > PubChem CIDs, cas numbers, compound names, etc.). > > On Thu, Jan 19, 2012 at 3:34 PM, Tamas Gunda tgunda2 . puma.unideb.hu < > owner-chemistry],[ccl.net> wrote: > >> >> Sent to CCL by: "Tamas Gunda" [tgunda2-.-puma.unideb.hu] >> Dear CCL members, >> >> A major upgrade of my e-review on chemical drawing programs was >> performed. >> ChemDoodle has been added, MarvinSketch has also been discussed in detai= l, >> and several small applications have been added and dead projects have >> been removed, etc. >> If you are interested have a look at: >> >> http://dragon.unideb.hu/~**gundat/rajzprogramok/dprog.**html >> >> Tamas Gunda >> >> >> >> -=3D This is automatically added to each message by the mailing script = =3D-** >> E-mail to subscribers: CHEMISTRY],[ccl.net or use: >> http://www.ccl.net/cgi-bin/**ccl/send_ccl_message >> >> E-mail to administrators: CHEMISTRY-REQUEST],[ccl.net or use >> http://www.ccl.net/cgi-bin/**ccl/send_ccl_message >> >> **http://www.ccl.net/chemistry/**sub_unsub.shtmlConferences: http://server.ccl.net/** >> chemistry/announcements/**conferences/ >> >> Search Messages: http://www.ccl.net/chemistry/**searchccl/index.shtml >> ** >> http://www.ccl.net/spammers.**txt >> >> RTFI: http://www.ccl.net/chemistry/**aboutccl/instructions/ >> >> >> > > > -- > Wolf-D. Ihlenfeldt - Xemistry GmbH - wdi],[xemistry.com > Phone: +49 6174 201455 - Fax +49 6174 209665 > --- > xemistry gmbh =96 Gesch=E4ftsf=FChrer/Managing Director: Dr. W. D. Ihlenf= eldt > Address: Hainholzweg 11, D-61462 K=F6nigstein, Germany > HR K=F6nigstein B7522 : Ust/VAT ID DE215316329 : DUNS 34-400-1719 > > --00151750e2d44b46b904b6f5f8cb Content-Type: text/html; charset=windows-1252 Content-Transfer-Encoding: quoted-printable Dear Tamas,

=A0=A0=A0=A0 I tried=A0 the "Xemistry Web Sketcher&= quot;, but the click response is too slow. I selected the button "sing= le bond" and clicked on the draw area,then it cost several seconds to = generate bond on the screen.=A0 I guess it may fetch something from the ser= ver instead of generating them by the client itself.=A0 Also, it made my IE= explore crashed two times!!=A0
=A0=A0=A0 I have to say "ChemWriter" is much better, since it is = fast and work well even on the IE6 explore.
=A0=A0=A0 Sorry for my terri= ble english.

Qiancheng


2012/1/= 19 Wolf Ihlenfeldt wdi/axemistry.com <= span dir=3D"ltr"><owner-chemi= stry=ccl.net>

Strangely, this revie= w is completely missing the technologically unique Web sketcher originally = developed for PubChem and accessible in an enhanced version at www.xemistry.com/= edit/frame.html

This tool is the only full-featured Web structure editor which is *not*= a plug-in (with all its platform and installation issues) nor a Java apple= t (with its own JVM engine presence and versioning problems, plus download = time issues). Compared to other Web editors of any kind, it can=A0 access a= much broader range of Internet structure databases directly (over 2 dozen = currently), and it supports a much larger list of I/O formats (for example,= it supports SDF3000 and original ChemDraw CDX/CDXML or ISISDraw skc/tgf fi= les as well as direct input and decoding of SMILES, SLN, JME strings, PubCh= em CIDs, cas numbers, compound names, etc.).

On Thu, Jan 19, 2012 at 3:= 34 PM, Tamas Gunda tgunda2 . puma.unideb.hu <owner-chemistry],[ccl.net>= wrote:
<= br> Sent to CCL by: "Tamas Gunda" [tgunda2-.-puma.unideb.hu]
Dear CCL members,

A major upgrade of my =A0e-review on chemical drawing programs was performe= d.
ChemDoodle has been added, MarvinSketch has also been discussed in detail,<= br> and several small applications have been added and dead projects have been = removed, etc.
If you are interested have a look at:

http://dragon.unideb.hu/~gundat/rajzprogramok/dprog.html

Tamas Gunda



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





= --
Wolf-D. Ihlenfeldt -=A0 Xemistry GmbH - wdi],[xemistry.com
Phone: +49 6174 20145= 5 - Fax +49 6174 209665
---
xemistry gmbh =96 Gesch=E4ftsf=FChrer/Managing Director: Dr. W. D. I= hlenfeldt
Address: Hainholzweg 11, D-61462 K=F6nigstein, Germany
HR K=F6nigstein B= 7522 : Ust/VAT ID DE215316329 : DUNS 34-400-1719


--00151750e2d44b46b904b6f5f8cb-- From owner-chemistry@ccl.net Fri Jan 20 11:01:00 2012 From: "Arne Dieckmann adieckma * googlemail.com" To: CCL Subject: CCL:G: Low frequencies Message-Id: <-46173-120120001805-27277-uP6aqdJraeWRpjFrLF0hqg,+,server.ccl.net> X-Original-From: Arne Dieckmann Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=us-ascii Date: Thu, 19 Jan 2012 21:17:51 -0800 Mime-Version: 1.0 (Apple Message framework v1251.1) Sent to CCL by: Arne Dieckmann [adieckma^^googlemail.com] Hi Gonzalo, I am aware of the problems related to accurately calculating free energies and I have carried out ab initio MD simulations to determine those for other projects. However, this time I need a good description of the electronic structure and cannot afford to use just a GGA functional to make dynamics feasable. To calculate partition functions for a limited number of vibrations you can use Gaussian's freqchk utility. It is clear from inspection of the underlying equations that inaccuracies of small frequencies introduce the largest error into the entropy terms. However, I was wondering why the HinderedRotor option did not change the results. It would be great to hear more about how people are dealing with this problem (maybe also some comments on the quasiharmonic approximation and if it can be applied in Gaussian). Cheers, Arne - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Dr. Arne Dieckmann Houk Research Lab | University of California, Los Angeles On Jan 19, 2012, at 5:32 PM, Gonzalo Jimenez Oses gjimenez**chem.ucla.edu wrote: > > Sent to CCL by: "Gonzalo Jimenez Oses" [gjimenez[*]chem.ucla.edu] > Dear Arne, > > Well, the problem is that, if I'm not wrong, you always need 3N-6 vibrations > in the ground state (3N-7 in the TS) for the vibrational/thermal analysis to > make sense. I guess you cannot simple get rid of an arbitrary number of > vibrations. This is the price you need to pay when calculating frequencies > of big and flexible molecules. More sophisticated methods to accurately > describe thermal/entropic contributions would involve dynamics, which, of > course is unfeasible at QM levels for most of our systems. > I've wrote a silly program to calculate the partition functions with any > nunmber of the calculated frequencies (overriding theory!), and I could > experience in my bones that the smallest frequencies contribute the most to > the thermal/entropic corrections. This means that you'll always have errors > when comparing related structures when moving from DeltaH to DeltaG, which, > yes, it's really annoying. > I guess that there is not a rule of thumb for this. Small (and not so small) > frequencies appear here and there, depending on the method (m06-2x in > gaussian is painful), solvent method, grid size, convergence criteria... This > is why DeltaG are so unrealistic when dealing with big molecules (but, yeah, > usually our bosses and referees want them, don't they?) > > Best, > > Gonzalo > > -------------------------------------------------- >> From: "Arne Dieckmann adieckma(-)googlemail.com" > Sent: Thursday, January 19, 2012 3:08 PM > To: "Oses, Gonzalo Jimenez " > Subject: CCL:G: Low frequencies > >> >> Sent to CCL by: Arne Dieckmann [adieckma#,#googlemail.com] >> Dear all, >> >> I am optimizing a series of quite large molecules (102 atoms, more than >> half of those are C,N,O) using the M062X functional. A closer look at the >> calculated frequencies reveals that 80 of 300 vibrations are below >> Gaussian's threshold of 625 cm^-1 for "low frequencies". I have repeated >> the frequency calculation using the HinderedRotor option, which produced >> exactly the same values for thermal corrections, although 26 vibrations >> were identified as really being rotations. In another calculation on the >> same system, I substracted the contribution of those 80 vibrations using >> the freqchk utility resulting in substantially different values for >> thermal corrections. Would you consider those values to be more reliable >> than the initial ones? >> >> >> Best regards, >> Arne >> >> - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - >> - - - - - - - - - - - - >> Dr. Arne Dieckmann >> Houk Research Lab | University of California, Los Angeles> > From owner-chemistry@ccl.net Fri Jan 20 11:36:00 2012 From: "Gerald Knizia knizia^-^Princeton.EDU" To: CCL Subject: CCL: G09: CCSD method and large basis Sets Message-Id: <-46174-120119231227-10436-vOmPpP6GxNqDAzwcAwuqhw+/-server.ccl.net> X-Original-From: Gerald Knizia Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 19 Jan 2012 23:11:53 -0500 MIME-Version: 1.0 Sent to CCL by: Gerald Knizia [knizia===Princeton.EDU] On 18.01.2012 11:05, Roger Robinson scu98rkr%a%gmail.com wrote: > But a I also need to calculate the barrier heights with as much > precision as possible. > [...] > > They suggest CCSD(T)/CBS+CV+Rel.//M06-2X/MG3S as a very accurate method. > > Im looking at slightly bigger molecules them and I probably dont have > the same resources available as them. You might also want to consider using Molpro for this task. Is has a very efficient CCSD(T) program and can do explicit correlations (CCSD(T)-F12). Using F12 you would probably get away with (partially) augmented double-zeta basis sets to get the basis set limit to within around 1--2kcal/mol. -- Gerald Knizia From owner-chemistry@ccl.net Fri Jan 20 12:10:00 2012 From: "Wolf Ihlenfeldt wdi:-:xemistry.com" To: CCL Subject: CCL: Chemical Drawing Programs review Message-Id: <-46175-120120105647-16946-GRN37/Jwo0g/DohHpkCG5g]*[server.ccl.net> X-Original-From: Wolf Ihlenfeldt Content-Type: multipart/alternative; boundary=002354470b4ce8a61004b6f7b97d Date: Fri, 20 Jan 2012 16:56:38 +0100 MIME-Version: 1.0 Sent to CCL by: Wolf Ihlenfeldt [wdi-.-xemistry.com] --002354470b4ce8a61004b6f7b97d Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable On Fri, Jan 20, 2012 at 2:50 PM, qiancheng shen qianchengshen%%gmail.com < owner-chemistry]_[ccl.net> wrote: > Dear Tamas, > > I tried the "Xemistry Web Sketcher", but the click response is too > slow. Yes, it is server-based. There is however an option to adjust the required bandwidth (upper left corner menu, the default is 'broadband' which may be too much for your location). The minimum bandwidth required is about the same as for Internet radio. So if you can listen to international radio stations over the Internet without hiccups and buffering phases in streaming mode, it should work fine in minimal bandwidth mode, but with connectivity below that, you may indeed have a problem. For normal users, response time should be more than adequate. It has been in use for years at PubChem without significant complaints. Fortunately such constraints become less and less of a problem even in remote locations. The same is true for the use of antique browsers such as your IE6 - which btw is still an officially supported system, with special consideration regarding image encoding, etc, - but only if your bandwidth is not exceeded. IE6 reacts nastily if image display requests queue up..The minimum IE version required by this software is actually IE4, which has really limited JS capabilities, and cannot even display PNG images. I selected the button "single bond" and clicked on the draw area,then it > cost several seconds to generate bond on the screen. I guess it may fetc= h > something from the server instead of generating them by the client itself= . > Also, it made my IE explore crashed two times!! > I have to say "ChemWriter" is much better, since it is fast and work > well even on the IE6 explore. > Sorry for my terrible english. > > Qiancheng > > > 2012/1/19 Wolf Ihlenfeldt wdi/axemistry.com > >> >> Strangely, this review is completely missing the technologically unique >> Web sketcher originally developed for PubChem and accessible in an enhan= ced >> version at www.xemistry.com/edit/frame.html >> >> This tool is the only full-featured Web structure editor which is *not* = a >> plug-in (with all its platform and installation issues) nor a Java apple= t >> (with its own JVM engine presence and versioning problems, plus download >> time issues). Compared to other Web editors of any kind, it can access = a >> much broader range of Internet structure databases directly (over 2 doze= n >> currently), and it supports a much larger list of I/O formats (for examp= le, >> it supports SDF3000 and original ChemDraw CDX/CDXML or ISISDraw skc/tgf >> files as well as direct input and decoding of SMILES, SLN, JME strings, >> PubChem CIDs, cas numbers, compound names, etc.). >> >> On Thu, Jan 19, 2012 at 3:34 PM, Tamas Gunda tgunda2 . puma.unideb.hu < >> owner-chemistry],[ccl.net> wrote: >> >>> >>> Sent to CCL by: "Tamas Gunda" [tgunda2-.-puma.unideb.hu] >>> Dear CCL members, >>> >>> A major upgrade of my e-review on chemical drawing programs was >>> performed. >>> ChemDoodle has been added, MarvinSketch has also been discussed in >>> detail, >>> and several small applications have been added and dead projects have >>> been removed, etc. >>> If you are interested have a look at: >>> >>> http://dragon.unideb.hu/~**gundat/rajzprogramok/dprog.**html >>> >>> Tamas Gunda >>> >>> >>> >>> -=3D This is automatically added to each message by the mailing script = =3D-* >>> * >>> E-mail to subscribers: CHEMISTRY],[ccl.net or use: >>> http://www.ccl.net/cgi-bin/**ccl/send_ccl_message >>> >>> E-mail to administrators: CHEMISTRY-REQUEST],[ccl.net or use >>> http://www.ccl.net/cgi-bin/**ccl/send_ccl_message >>> >>> **http://www.ccl.net/chemistry/**sub_unsub.shtmlConferences: http://server.ccl.net/** >>> chemistry/announcements/**conferences/ >>> >>> Search Messages: http://www.ccl.net/chemistry/**searchccl/index.shtml >>> ** >>> http://www.ccl.net/spammers.**txt >>> >>> RTFI: http://www.ccl.net/chemistry/**aboutccl/instructions/ >>> >>> >>> >> >> >> -- >> Wolf-D. Ihlenfeldt - Xemistry GmbH - wdi],[xemistry.com >> Phone: +49 6174 201455 - Fax +49 6174 209665 >> --- >> xemistry gmbh =E2=80=93 Gesch=C3=A4ftsf=C3=BChrer/Managing Director: Dr.= W. D. Ihlenfeldt >> Address: Hainholzweg 11, D-61462 K=C3=B6nigstein, Germany >> HR K=C3=B6nigstein B7522 : Ust/VAT ID DE215316329 : DUNS 34-400-1719 >> >> > --=20 Wolf-D. Ihlenfeldt - Xemistry GmbH - wdi]_[xemistry.com Phone: +49 6174 201455 - Fax +49 6174 209665 --- xemistry gmbh =E2=80=93 Gesch=C3=A4ftsf=C3=BChrer/Managing Director: Dr. W.= D. Ihlenfeldt Address: Hainholzweg 11, D-61462 K=C3=B6nigstein, Germany HR K=C3=B6nigstein B7522 : Ust/VAT ID DE215316329 : DUNS 34-400-1719 --002354470b4ce8a61004b6f7b97d Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable

On Fri, Jan 20, 2012 at 2:50 PM, qianche= ng shen qianchengshen%%gmail.com <owner-chemistry]_[ccl= .net> wrote:
Dear Tamas,

=C2=A0= =C2=A0=C2=A0=C2=A0 I tried=C2=A0 the "Xemistry Web Sketcher", but= the click response is too slow.

Yes, it is server-based. There is however an option to adjust the = required bandwidth (upper left corner menu, the default is 'broadband&#= 39; which may be too much for your location). The minimum bandwidth require= d is about the same as for Internet radio. So if you can listen to internat= ional radio stations over the Internet without hiccups and buffering phases= in streaming mode, it should work fine in minimal bandwidth mode, but with= connectivity below that, you may indeed have a problem. For normal users, = response time should be more than adequate. It has been in use for years at= PubChem without significant complaints.

Fortunately such constraints become less and less of a problem even in = remote locations. The same is true for the use of antique browsers such as = your IE6 - which btw is still an officially supported system, with special = consideration regarding image encoding, etc, - but only if your bandwidth i= s not exceeded. IE6 reacts nastily if image display requests queue up..The = minimum IE version required by this software is actually IE4, which has rea= lly limited JS capabilities, and cannot even display PNG images.


I selected= the button "single bond" and clicked on the draw area,then it co= st several seconds to generate bond on the screen.=C2=A0 I guess it may fet= ch something from the server instead of generating them by the client itsel= f.=C2=A0 Also, it made my IE explore crashed two times!!=C2=A0
=C2=A0=C2=A0=C2=A0 I have to say "ChemWriter" is much better, sin= ce it is fast and work well even on the IE6 explore.
=C2=A0=C2=A0=C2=A0 = Sorry for my terrible english.

Qiancheng


2012/1/19 Wolf Ihlenfeldt wdi/axemistry.com <owner-chemistry:-:ccl.net&= gt;

Strangely, this revie= w is completely missing the technologically unique Web sketcher originally = developed for PubChem and accessible in an enhanced version at www.xemistry.com/= edit/frame.html

This tool is the only full-featured Web structure editor which is *not*= a plug-in (with all its platform and installation issues) nor a Java apple= t (with its own JVM engine presence and versioning problems, plus download = time issues). Compared to other Web editors of any kind, it can=C2=A0 acces= s a much broader range of Internet structure databases directly (over 2 doz= en currently), and it supports a much larger list of I/O formats (for examp= le, it supports SDF3000 and original ChemDraw CDX/CDXML or ISISDraw skc/tgf= files as well as direct input and decoding of SMILES, SLN, JME strings, Pu= bChem CIDs, cas numbers, compound names, etc.).

On Thu, Jan 19, 2012 at 3:34 PM, Tamas = Gunda tgunda2 . puma.un= ideb.hu <owner-chemistry],[ccl.net> wrote:

Sent to CCL by: "Tamas Gunda" [tgunda2-.-puma.unideb.hu]
Dear CCL members,

A major upgrade of my =C2=A0e-review on chemical drawing programs was perfo= rmed.
ChemDoodle has been added, MarvinSketch has also been discussed in detail,<= br> and several small applications have been added and dead projects have been = removed, etc.
If you are interested have a look at:

http://dragon.unideb.hu/~gundat/rajzprogramok/dprog.html

Tamas Gunda



-=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 http://www.ccl.net/cgi-bin/ccl/send_ccl_message

E-mail to administrators: CHEMISTRY-REQUEST],[ccl.net or use
=C2=A0 =C2=A0 http://www.ccl.net/cgi-bin/ccl/send_ccl_message



--
Wolf-D. Ihlenfeldt -= =C2=A0 Xemistry GmbH - wdi],[xemistry.com
Phone: +49 6174 201455 - Fax +49 6174 209665
---
xemistry gmbh =E2=80=93 Gesch=C3=A4ftsf=C3=BChrer/Managing Director:= Dr. W. D. Ihlenfeldt
Address: Hainholzweg 11, D-61462 K=C3=B6nigstein, Germany
HR K=C3=B6nigs= tein B7522 : Ust/VAT ID DE215316329 : DUNS 34-400-1719





--
Wolf-D. Ihlenfeldt -=C2= =A0 Xemistry GmbH - w= di]_[xemistry.com
Phone: +49 6174 201455 - Fax +49 6174 209665
---<= br>xemistry gmbh =E2=80=93 Gesch=C3=A4ftsf=C3=BChrer/Managing Director: Dr.= W. D. Ihlenfeldt
Address: Hainholzweg 11, D-61462 K=C3=B6nigstein, Germany
HR K=C3=B6nigs= tein B7522 : Ust/VAT ID DE215316329 : DUNS 34-400-1719

--002354470b4ce8a61004b6f7b97d-- From owner-chemistry@ccl.net Fri Jan 20 18:42:00 2012 From: "Roger Robinson scu98rkr^^gmail.com" To: CCL Subject: CCL: G09: CCSD method and large basis Sets Message-Id: <-46176-120119075305-26751-+tfAF2FVONKn1f6SCfcotg]=[server.ccl.net> X-Original-From: Roger Robinson Content-Type: multipart/alternative; boundary="------------090207060808090504020303" Date: Thu, 19 Jan 2012 12:52:57 +0000 MIME-Version: 1.0 Sent to CCL by: Roger Robinson [scu98rkr__gmail.com] This is a multi-part message in MIME format. --------------090207060808090504020303 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Hi Sebastian, Thanks for taking your time to reply. Im currently reading through your paper DSD-PBEP86: in search of the best double-hybrid DFT with spin-component scaled MP2 and dispersion corrections and trying a few tests out. I might be back to ask a few more questions later. Cheers Roger > A good compromise between accuracy and timing is achieved with double > hybrid DFT. Usually much more accurate than hybrid functionals, and > for sure much faster than couple cluster. However, if you need > chemical accuracy (~1 kcal/mol) you should first compare them to > CCSD(T)/CBS with a small model system. And always pray that you don't > have big non-dynamic correlation, or even couple cluster will be a > failure! > xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx > ..........Sebastian Kozuch........... > xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx > ....Weizmann Institute of Science.... > ...........Rehovot, Israel........... > .. sebastian.kozuch()weizmann.ac.il .. > http://yfaat.ch.huji.ac.il/kozuch.htm > xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx > ------------------------------------------------------------------------ > *From:* Roger Robinson scu98rkr%a%gmail.com > *To:* "Kozuch, Sebastian " > *Sent:* Wednesday, January 18, 2012 6:05 PM > *Subject:* CCL: G09: CCSD method and large basis Sets > > > Sent to CCL by: Roger Robinson [scu98rkr^-^gmail.com] > Dear All, > > I want to accurately calculate barrier heights for several sets of > reactions. > > I am looking at molecules up to say 9-10 large atoms + Hydrogens. > Currently I am using G09 for my calculations > > For most of my work I am looking at using the M06-2X functional for > calculating geometries, frequencies and zero point energies and for > other bits and bobs. > > I have just about managed to install GAMESS and I am considering maybe > the M08-SO functional for future work. > > But a I also need to calculate the barrier heights with as much > precision as possible. > > I have looked at a few papers such as > > Kinetics of hydrogen-transfer isomerizations of butoxyl radicals by > Zhen and Truhlar > > They suggest CCSD(T)/CBS+CV+Rel.//M06-2X/MG3S as a very accurate method. > > Im looking at slightly bigger molecules them and I probably dont have > the same resources available as them. > > I have managed to calculate barrier heights at the > CCSD(T)/aug-cc-pVDZ//M06-2X/MG3S level so far. > I am currently trying to do so at the CCSD(T)/aug-cc-pVTZ//M06-2X/MG3S > level. > > So far the RWF files have got to ~330GB ! Im not too sure I have the > resources to do this. > > The Timings Comparisons on http://cccbdb.nist.gov/ > > Seem to suggest VTZ will be 42 slower for a molecule with 3 large > atoms, which does nt sound right to me. This might be becuase the > examples on http://cccbdb.nist.gov/ run quite quickly so there is alot > of I/O activity ? > > 42 times longer would be well beyond my capabilities. > > Does anyone have any though on CCSD(T)/maug-cc-pVTZ or CCSD(T)/cc-VTZ. > > Would CCSD(T)/aug-cc-pVDZ//M06-2X/MG3S be about as accurate as Im > going to get for a molecule with 9 carbons ? > I can use 12 core machine shared memory machines but Im hoping the > jobs last weeks not months. > > Any help appreciated, > > Roger> the strange characters on the top line to the () sign. You can also > > > E-mail to subscribers: CHEMISTRY()ccl.net > or use: > > > E-mail to administrators: CHEMISTRY-REQUEST()ccl.net > or use> > > > > > --------------090207060808090504020303 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Hi Sebastian,

Thanks for taking your time to reply.

Im currently reading through your paper

DSD-PBEP86: in search of the best double-hybrid DFT with
spin-component scaled MP2 and dispersion corrections

and trying a few tests out. I might be back to ask a few more questions later.

Cheers Roger


A good compromise between accuracy and timing is achieved with double hybrid DFT. Usually much more accurate than hybrid functionals, and for sure much faster than couple cluster. However, if you need chemical accuracy (~1 kcal/mol) you should first compare them to CCSD(T)/CBS with a small model system. And always pray that you don't have big non-dynamic correlation, or even couple cluster will be a failure!
 
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
..........Sebastian Kozuch...........
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
....Weizmann Institute of Science....
...........Rehovot, Israel...........
.. sebastian.kozuch()weizmann.ac.il ..
http://yfaat.ch.huji.ac.il/kozuch.htm
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
From: Roger Robinson scu98rkr%a%gmail.com <owner-chemistry()ccl.net>
To: "Kozuch, Sebastian " <kozuchs()yahoo.com>
Sent: Wednesday, January 18, 2012 6:05 PM
Subject: CCL: G09: CCSD method and large basis Sets


Sent to CCL by: Roger Robinson [scu98rkr^-^gmail.com]
Dear All,

I want to accurately calculate barrier heights for several sets of reactions.

I am looking at molecules up to say 9-10 large atoms + Hydrogens. Currently I am using G09 for my calculations

For most of my work I am looking at using the M06-2X functional for calculating geometries, frequencies and zero point energies and for other bits and bobs.

I have just about managed to install GAMESS and I am considering maybe the M08-SO functional for future work.

But a I also need to calculate the barrier heights with as much precision as possible.

I have looked at a few papers such as

Kinetics of hydrogen-transfer isomerizations of butoxyl radicals by Zhen and Truhlar

They suggest CCSD(T)/CBS+CV+Rel.//M06-2X/MG3S as a very accurate method.

Im looking at slightly bigger molecules them and I probably dont have the same resources available as them.

I have managed to calculate barrier heights at the CCSD(T)/aug-cc-pVDZ//M06-2X/MG3S level so far.
I am currently trying to do so at the CCSD(T)/aug-cc-pVTZ//M06-2X/MG3S level.

So far the RWF files have got to ~330GB ! Im not too sure I have the resources to do this.

The Timings Comparisons on http://cccbdb.nist.gov/

Seem to suggest VTZ will be 42 slower for a molecule with 3 large atoms, which does nt sound right to me. This might be becuase the examples on http://cccbdb.nist.gov/ run quite quickly so there is alot of I/O activity ?

42 times longer would be well beyond my capabilities.

Does anyone have any though on  CCSD(T)/maug-cc-pVTZ or CCSD(T)/cc-VTZ.

Would CCSD(T)/aug-cc-pVDZ//M06-2X/MG3S be about as accurate as Im going to get for a molecule with 9 carbons ?
I can use 12 core machine shared memory machines but Im hoping the jobs last weeks not months.

Any help appreciated,

Roger


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--------------090207060808090504020303-- From owner-chemistry@ccl.net Fri Jan 20 19:17:00 2012 From: "maxim totrov max.:.molsoft.com" To: CCL Subject: CCL: Chemical Drawing Programs review Message-Id: <-46177-120120134548-10509-rhXaKTe4N1/tpXOmN6VPyQ]|[server.ccl.net> X-Original-From: maxim totrov Content-Type: multipart/alternative; boundary=Apple-Mail-28-885587595 Date: Fri, 20 Jan 2012 10:45:38 -0800 Mime-Version: 1.0 (Apple Message framework v936) Sent to CCL by: maxim totrov [max(0)molsoft.com] --Apple-Mail-28-885587595 Content-Type: text/plain; charset=WINDOWS-1252; format=flowed; delsp=yes Content-Transfer-Encoding: quoted-printable > > Yes, it is server-based. There is however an option to adjust the =20 > required bandwidth (upper left corner menu, the default is =20 > 'broadband' which may be too much for your location). The minimum =20 > bandwidth required is about the same as for Internet radio. So if =20 > you can listen to international radio stations over the Internet =20 > without hiccups and buffering phases in streaming mode, it should =20 > work fine in minimal bandwidth mode, but with connectivity below =20 > that, you may indeed have a problem. For normal users, response time =20= > should be more than adequate. It has been in use for years at =20 > PubChem without significant complaints. > Wolf, i would think that the issue is latency rather than bandwidth. A =20= 10Mb link can have latencies in the hundreds of milliseconds - movies =20= would play just fine but server-based applets can still be a pain. =20 Just my 2 cents... Max Totrov > Fortunately such constraints become less and less of a problem even =20= > in remote locations. The same is true for the use of antique =20 > browsers such as your IE6 - which btw is still an officially =20 > supported system, with special consideration regarding image =20 > encoding, etc, - but only if your bandwidth is not exceeded. IE6 =20 > reacts nastily if image display requests queue up..The minimum IE =20 > version required by this software is actually IE4, which has really =20= > limited JS capabilities, and cannot even display PNG images. > > > I selected the button "single bond" and clicked on the draw =20 > area,then it cost several seconds to generate bond on the screen. I =20= > guess it may fetch something from the server instead of generating =20 > them by the client itself. Also, it made my IE explore crashed two =20= > times!! > I have to say "ChemWriter" is much better, since it is fast and =20= > work well even on the IE6 explore. > Sorry for my terrible english. > > Qiancheng > > > 2012/1/19 Wolf Ihlenfeldt wdi/axemistry.com chemistry:-:ccl.net> > > Strangely, this review is completely missing the technologically =20 > unique Web sketcher originally developed for PubChem and accessible =20= > in an enhanced version at www.xemistry.com/edit/frame.html > > This tool is the only full-featured Web structure editor which is =20 > *not* a plug-in (with all its platform and installation issues) nor =20= > a Java applet (with its own JVM engine presence and versioning =20 > problems, plus download time issues). Compared to other Web editors =20= > of any kind, it can access a much broader range of Internet =20 > structure databases directly (over 2 dozen currently), and it =20 > supports a much larger list of I/O formats (for example, it supports =20= > SDF3000 and original ChemDraw CDX/CDXML or ISISDraw skc/tgf files as =20= > well as direct input and decoding of SMILES, SLN, JME strings, =20 > PubChem CIDs, cas numbers, compound names, etc.). > > On Thu, Jan 19, 2012 at 3:34 PM, Tamas Gunda tgunda2 . =20 > puma.unideb.hu wrote: > > Sent to CCL by: "Tamas Gunda" [tgunda2-.-puma.unideb.hu] > Dear CCL members, > > A major upgrade of my e-review on chemical drawing programs was =20 > performed. > ChemDoodle has been added, MarvinSketch has also been discussed in =20 > detail, > and several small applications have been added and dead projects =20 > have been removed, etc. > If you are interested have a look at: > > http://dragon.unideb.hu/~gundat/rajzprogramok/dprog.html > > Tamas Gunda > > > > -=3D This is automatically added to each message by the mailing script = =20 > =3D- > E-mail to subscribers: CHEMISTRY],[ccl.net or use:> > E-mail to administrators: CHEMISTRY-REQUEST],[ccl.net or useConferences: = http://server.ccl.net/chemistry/announcements/conferences/> > > > > > --=20 > Wolf-D. Ihlenfeldt - Xemistry GmbH - wdi],[xemistry.com > Phone: +49 6174 201455 - Fax +49 6174 209665 > --- > xemistry gmbh =96 Gesch=E4ftsf=FChrer/Managing Director: Dr. W. D. =20 > Ihlenfeldt > Address: Hainholzweg 11, D-61462 K=F6nigstein, Germany > HR K=F6nigstein B7522 : Ust/VAT ID DE215316329 : DUNS 34-400-1719 > > > > > > --=20 > Wolf-D. Ihlenfeldt - Xemistry GmbH - wdi---xemistry.com > Phone: +49 6174 201455 - Fax +49 6174 209665 > --- > xemistry gmbh =96 Gesch=E4ftsf=FChrer/Managing Director: Dr. W. D. =20 > Ihlenfeldt > Address: Hainholzweg 11, D-61462 K=F6nigstein, Germany > HR K=F6nigstein B7522 : Ust/VAT ID DE215316329 : DUNS 34-400-1719 > --Apple-Mail-28-885587595 Content-Type: text/html; charset=WINDOWS-1252 Content-Transfer-Encoding: quoted-printable

Yes, it is = server-based. There is however an option to adjust the required = bandwidth (upper left corner menu, the default is 'broadband' which may = be too much for your location). The minimum bandwidth required is about = the same as for Internet radio. So if you can listen to international = radio stations over the Internet without hiccups and buffering phases in = streaming mode, it should work fine in minimal bandwidth mode, but with = connectivity below that, you may indeed have a problem. For normal = users, response time should be more than adequate. It has been in use = for years at PubChem without significant complaints.
=

Wolf, i would think = that the issue is latency rather than bandwidth. A 10Mb link can have = latencies in the hundreds of milliseconds - movies would play just fine = but server-based applets can still be a pain. Just my 2 = cents...

Max = Totrov



Fortunately such = constraints become less and less of a problem even in remote locations. = The same is true for the use of antique browsers such as your IE6 - = which btw is still an officially supported system, with special = consideration regarding image encoding, etc, - but only if your = bandwidth is not exceeded. IE6 reacts nastily if image display requests = queue up..The minimum IE version required by this software is actually = IE4, which has really limited JS capabilities, and cannot even display = PNG images.


I selected the button "single bond" = and clicked on the draw area,then it cost several seconds to generate = bond on the screen.  I guess it may fetch something from the server = instead of generating them by the client itself.  Also, it made my = IE explore crashed two times!! 
    I have to = say "ChemWriter" is much better, since it is fast and work well even on = the IE6 explore.
    Sorry for my terrible = english.

Qiancheng


2012/1/19 = Wolf Ihlenfeldt wdi/axemistry.com <owner-chemistry:-:ccl.net>
=

Strangely, this review is = completely missing the technologically unique Web sketcher originally = developed for PubChem and accessible in an enhanced version at www.xemistry.com/edit/frame.html

This tool = is the only full-featured Web structure editor which is *not* a plug-in = (with all its platform and installation issues) nor a Java applet (with = its own JVM engine presence and versioning problems, plus download time = issues). Compared to other Web editors of any kind, it can  access = a much broader range of Internet structure databases directly (over 2 = dozen currently), and it supports a much larger list of I/O formats (for = example, it supports SDF3000 and original ChemDraw CDX/CDXML or ISISDraw = skc/tgf files as well as direct input and decoding of SMILES, SLN, JME = strings, PubChem CIDs, cas numbers, compound names, etc.).

On Thu, Jan 19, 2012 at 3:34 PM, Tamas Gunda = tgunda2 . puma.unideb.hu <owner-chemistry],[ccl.net> wrote:
=

= Sent to CCL by: "Tamas Gunda" [tgunda2-.-puma.unideb.hu]
Dear CCL members,

A = major upgrade of my  e-review on chemical drawing programs was = performed.
ChemDoodle has been added, MarvinSketch has also been = discussed in detail,
and several small applications have been added = and dead projects have been removed, etc.
If you are interested have = a look at:

http://dragon.unideb.hu/~gundat/rajzprogramok/dpr= og.html

Tamas Gunda



-=3D This is = automatically added to each message by the mailing script =3D- =
E-mail to subscribers: CHEMISTRY],[ccl.net or use:
    http://www.ccl.net/cgi-bin/ccl/send_ccl_message

E-mail to administrators: CHEMISTRY-REQUEST],[ccl.net or use
  =   http://www.ccl.net/cgi-bin/ccl/send_ccl_message



--
Wolf-D. Ihlenfeldt -  Xemistry GmbH - = wdi],[xemistry.com
Phone: +49 6174 201455 - Fax +49 6174 209665
---
xemistry gmbh =96 = Gesch=E4ftsf=FChrer/Managing Director: Dr. W. D. Ihlenfeldt
Address: = Hainholzweg 11, D-61462 K=F6nigstein, Germany
HR K=F6nigstein B7522 : = Ust/VAT ID DE215316329 : DUNS 34-400-1719

=




--
Wolf-D. Ihlenfeldt -  Xemistry GmbH - wdi---xemistry.com
Phone: +49 6174 201455 - Fax = +49 6174 209665
---
xemistry gmbh =96 Gesch=E4ftsf=FChrer/Managing = Director: Dr. W. D. Ihlenfeldt
Address: Hainholzweg 11, D-61462 = K=F6nigstein, Germany
HR K=F6nigstein B7522 : Ust/VAT ID DE215316329 = : DUNS 34-400-1719


= --Apple-Mail-28-885587595-- From owner-chemistry@ccl.net Fri Jan 20 19:52:00 2012 From: "jacqueline cawthray jcawth01[-]chem.ubc.ca" To: CCL Subject: CCL: Comparing molecules using MEP Message-Id: <-46178-120120150813-15087-ff+hO6x7t1ci9eNNFkVyZw()server.ccl.net> X-Original-From: "jacqueline cawthray" Date: Fri, 20 Jan 2012 15:08:12 -0500 Sent to CCL by: "jacqueline cawthray" [jcawth01 _ chem.ubc.ca] I am interested in the differences between binding of two metals to the same ligand using electrostatic mapping (g09 and gaussview). If I wish to compare the two, does the "scale" need to be the same for both? Sorry if this is a silly question. Jacquie