From owner-chemistry@ccl.net Tue Aug 26 07:10:00 2008 From: "Orlin Blajiev blajiev^vub.ac.be" To: CCL Subject: CCL:G: End of a frequency job Message-Id: <-37624-080826065823-5269-aERxtpUKX4xYXe9TyM+ojQ#server.ccl.net> X-Original-From: Orlin Blajiev Date: Tue, 26 Aug 2008 12:19:56 +0200 (CEST) Sent to CCL by: Orlin Blajiev [blajiev*vub.ac.be] Obviously the difference here is between the orthodox and the possible. Seems, however, that if a smaller and larger set come to one and the same optimized geometry then the frequencies calculated with the larger set on the structure from the smaller one would be correct. In this sense there is not stationary point for the method but ones which are closer to the truth and which are not. Anyway, in my system I have 17 heavy atoms in an organic molecule and 12 Ag as a metal "substrate". Additionally, the the system is charged. It needs to go through about hundreds of optimization steps. Doing this with 6-31+G** is rather time consuming. As far as understand the problem, it is not as much about the two different BS but about the goodness of the first one. (There was an article in Chemical Reviews which concluded that 4-31 is already a good set for geometry). If it drives the structural optimization into or near ( I guess that with large systems we have to loose it a little bit) a proper point it is OK. This must be my case as I do not have negative frequencies. Regards, Orlin >Sent to CCL by: Brian Salter-Duke [brian.james.duke[-]gmail.com] >errol lewars elewars+*+trentu.ca wrote: >> >> Sent to CCL by: errol lewars [elewars-#-trentu.ca] >> 2008 August 25 >> >> The general view is that it is simply wrong to use one method/basis for >> the optimization and another for the frequencies: consult some standard >> books on computational chemistry. >> >> E. Lewars >> === > >Yes, it is indeed wrong. If you do a frequency calculation at a geometry >which is not a stationary point for the method and basis set employed >for the frequency calculation, then the calculated frequencies do not >mean anything. You do not have the 6 nominally zero frequencies >corresponding to rotations and vibrations. It is quite likely that you >will not be able to identify those 6 and you may have imaginary >frequencies even if the original optimization was to a local minimum. > >Brian. > >> >> Close, David M. CLOSED^mail.etsu.edu wrote: >> >>> Sent to CCL by: "Close, David M." [CLOSED__mail.etsu.edu] >>> Yes, that is exactly right. As a check you could try a frequency calc. >>> using the same basis set. Usually 3 out of 4 of the "yes" are ok. For >>> some reason the third "yes" is sometimes a "no". I don't know why. >>> Now a more basic question. If you are taking a course on doing >>> calculations, you are always told you must use the same basis sets in >>> frequency calculations as on the original optimizations. But people >>> seem to be getting away from this are very large calculations. If it >>> takes a week to do an optimization, it might take 3-4 weeks to do a >>> frequency calculation. So people are now using smaller basis sets to do >>> faster frequency calcs. I do not happen to know if this leads to >>> problems. I do know that Berny Schlegel warned about this some time >>> ago, but I do not know the current thinking on this. >>> >>> >>> -----Original Message----- >>> >>> >>>> From: owner-chemistry ~~ ccl.net [mailto:owner-chemistry ~~ ccl.net] >>> Sent: Monday, August 25, 2008 11:29 AM >>> To: Close, David M. >>> Subject: CCL:G: End of a frequency job >>> >>> >>> Sent to CCL by: Orlin Blajiev [Orlin.Blajiev,vub.ac.be] >>> David, Alcides, >>> >>> >>> >>> Thanks for the info. I guess G03 reports the geometry as non-converged >>> >>> because I use different BS in Opt and Freq. >>> >>> Best regards, >>> Orlin >>> >>> >>> Alcides Simao alsimao[#]gmail.com wrote: >>> >>> >>>> Orlin: >>>> >>>> This is a routine check from GAUSSIAN, made after *all* frequency >>>> jobs. You can safely discart it. Gaussian will always do that, even if >>>> >>> >>> >>> >>>> you don't flag the 'OPT' option. >>>> >>>> Best, >>>> >>>> Alcideshttp://www.ccl.net/chemistry/sub_unsub.shtmlConferences: >> http://server.ccl.net/chemistry/announcements/conferences/> > >-- > Brian Salter-Duke (Brian Duke) Brian.James.Duke,+,gmail.com > Post: 626 Melbourne Rd, Spotswood, VIC, 3015, Australia > http://www.salter-duke.bigpondhosting.com/brian/index.htm >Honorary Researcher Fellow, Monash Institute of Pharmaceutical Sciences> > > > Orlin Blajiev Department of Metallurgy, Electrochemistry and Materials Science Faculty of Applied Science Vrije Universiteit Brussel Pleinlaan 2, B-1050 Brussels Belgium http://www.vub.ac.be/META/ tel.: 32-(0)2-6293538 fax : 32-(0)2-6293200 From owner-chemistry@ccl.net Tue Aug 26 08:04:01 2008 From: "Pascal Boulet pascal.boulet#univ-provence.fr" To: CCL Subject: CCL:G: End of a frequency job Message-Id: <-37625-080825152140-12045-0Z7+jbSqWtt9gqWMQqMaaA-x-server.ccl.net> X-Original-From: Pascal Boulet Content-Type: multipart/alternative; boundary="------------010105060909070605070607" Date: Mon, 25 Aug 2008 20:48:11 +0200 MIME-Version: 1.0 Sent to CCL by: Pascal Boulet [pascal.boulet],[univ-provence.fr] This is a multi-part message in MIME format. --------------010105060909070605070607 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit hello, It sounds strange to me that some people are using different basis sets for optimization and frequency calculations. In principle, the geometry is no longer at the minimum of the PES when the BS is changed, and in the case of frequency jobs, one can get imaginary frequencies. Pascal Close, David M. CLOSED^mail.etsu.edu wrote: > Sent to CCL by: "Close, David M." [CLOSED__mail.etsu.edu] > Yes, that is exactly right. As a check you could try a frequency calc. > using the same basis set. Usually 3 out of 4 of the "yes" are ok. For > some reason the third "yes" is sometimes a "no". I don't know why. > Now a more basic question. If you are taking a course on doing > calculations, you are always told you must use the same basis sets in > frequency calculations as on the original optimizations. But people > seem to be getting away from this are very large calculations. If it > takes a week to do an optimization, it might take 3-4 weeks to do a > frequency calculation. So people are now using smaller basis sets to do > faster frequency calcs. I do not happen to know if this leads to > problems. I do know that Berny Schlegel warned about this some time > ago, but I do not know the current thinking on this. > > > -----Original Message----- > >> From: owner-chemistry ~~ ccl.net [mailto:owner-chemistry ~~ ccl.net] >> > Sent: Monday, August 25, 2008 11:29 AM > To: Close, David M. > Subject: CCL:G: End of a frequency job > > > Sent to CCL by: Orlin Blajiev [Orlin.Blajiev,vub.ac.be] > David, Alcides, > > > > Thanks for the info. I guess G03 reports the geometry as non-converged > > because I use different BS in Opt and Freq. > > Best regards, > Orlin > > > Alcides Simao alsimao[#]gmail.com wrote: > >> Orlin: >> >> This is a routine check from GAUSSIAN, made after *all* frequency >> jobs. You can safely discart it. Gaussian will always do that, even if >> > > >> you don't flag the 'OPT' option. >> >> Best, >> >> Alcides >> > > > -- Dr. Pascal Boulet, Computational Chemist University of Provence Laboratoire Chimie Provence, UMR6264 Centre Saint-Jerome, case MADIREL F-13397 MARSEILLE Cedex 20, France Tel. +33 (0) 491 63 71 17 Fax. +33 (0) 491 63 71 11 courriel: pascal.boulet|,|univ-provence.fr http://www.lc-provence.fr http://allos.up.univ-mrs.fr/boulet --------------010105060909070605070607 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit hello,

It sounds strange to me that some people are using different basis sets for optimization and frequency calculations. In principle, the geometry is no longer at the minimum of the PES when the BS is changed, and in the case of frequency jobs, one can get imaginary frequencies.

Pascal

Close, David M. CLOSED^mail.etsu.edu wrote:
Sent to CCL by: "Close, David M." [CLOSED__mail.etsu.edu]
Yes, that is exactly right.  As a check you could try a frequency calc.
using the same basis set.  Usually 3 out of 4 of the "yes" are ok.  For
some reason the third "yes" is sometimes a "no".  I don't know why.
Now a more basic question.  If you are taking a course on doing
calculations, you are always told you must use the same basis sets in
frequency calculations as on the original optimizations.  But people
seem to be getting away from this are very large calculations.  If it
takes a week to do an optimization, it might take 3-4 weeks to do a
frequency calculation.  So people are now using smaller basis sets to do
faster frequency calcs.  I do not happen to know if this leads to
problems.  I do know that Berny Schlegel warned about this some time
ago, but I do not know the current thinking on this.


-----Original Message-----
  
From: owner-chemistry ~~ ccl.net [mailto:owner-chemistry ~~ ccl.net] 
    
Sent: Monday, August 25, 2008 11:29 AM
To: Close, David M.
Subject: CCL:G: End of a frequency job


Sent to CCL by: Orlin Blajiev [Orlin.Blajiev,vub.ac.be]
David, Alcides,



Thanks for the info. I guess  G03 reports the geometry as  non-converged

because I use different  BS in Opt and  Freq.

Best regards,
Orlin


Alcides Simao alsimao[#]gmail.com wrote:
  
Orlin:

This is a routine check from GAUSSIAN, made after *all* frequency 
jobs. You can safely discart it. Gaussian will always do that, even if
    

  
you don't flag the 'OPT' option.

Best,

Alcides
    


  

-- 
Dr. Pascal Boulet, Computational Chemist
University of Provence
Laboratoire Chimie Provence, UMR6264
Centre Saint-Jerome, case MADIREL
F-13397 MARSEILLE Cedex 20, France
Tel. +33 (0) 491 63 71 17 Fax. +33 (0) 491 63 71 11
courriel: pascal.boulet|,|univ-provence.fr
http://www.lc-provence.fr
http://allos.up.univ-mrs.fr/boulet
--------------010105060909070605070607-- From owner-chemistry@ccl.net Tue Aug 26 08:39:00 2008 From: "Mr shabbir shabbir!^!nenu.edu.cn" To: CCL Subject: CCL: 2nd time Chemdraw2002 Message-Id: <-37626-080826083107-16678-eKs0HrPPeKh2L1eJ1ZBKBA : server.ccl.net> X-Original-From: "Mr shabbir" Date: Tue, 26 Aug 2008 08:31:03 -0400 Sent to CCL by: "Mr shabbir" [shabbir * nenu.edu.cn] Hi I am using chemdraw2002.When I trasferred by pasting a figure to chemdraw window that figure changes its color and some bad spots apear on it.I used many ways but no effect.Any body now how to paste figure in chmdraw so that it can not change its orginality. Highly appreciating the answer Mr Shabbir shabbir%a%nenu.edu.cn From owner-chemistry@ccl.net Tue Aug 26 10:59:01 2008 From: "Toomas Tamm tt-ccl2\a/yki.ttu.ee" To: CCL Subject: CCL: End of a frequency job Message-Id: <-37627-080826035848-8772-RwpEagErFwFbICpQH7r4ng#%#server.ccl.net> X-Original-From: Toomas Tamm Content-Transfer-Encoding: 7bit Content-Type: text/plain Date: Tue, 26 Aug 2008 10:01:41 +0300 Mime-Version: 1.0 Sent to CCL by: Toomas Tamm [tt-ccl2=yki.ttu.ee] On Mon, 2008-08-25 at 13:46 -0400, Close, David M. CLOSED^mail.etsu.edu wrote: > Now a more basic question. If you are taking a course on doing > calculations, you are always told you must use the same basis sets in > frequency calculations as on the original optimizations. But people > seem to be getting away from this are very large calculations. If it > takes a week to do an optimization, it might take 3-4 weeks to do a > frequency calculation. So people are now using smaller basis sets to do > faster frequency calcs. On several occasions, we have re-optimized the structure with a smaller basis set, checked that no significant changes in geometry have occurred (usually the gradients at initial optimization step, and the number of additional steps needed, are good diagnostics, too), and then performed a frequency calculation for the re-optimized geometry, using the smaller basis set. We have even used the zero-point energies from such calculations together with electronic energies from the large-basis calculations. I believe this is theoretically correct, just less accurate than calculating the frequencies with the larger basis set. Of course there remains the slight possiblity that the large-basis-set geometry was a transition state while the small-basis-set geometry is a minimum. We have considered the risk small enough given the savings in computation time. Any comments on this procedure? -- Toomas Tamm e-mail: tt-ccl2 (at) kky . ttu . ee Chair of Inorganic Chemistry voice: INT+372-620-2810 Tallinn University of Technology fax: INT+372-620-2828 Ehitajate tee 5, EE-19086 Tallinn, Estonia http://www.kk.ttu.ee/toomas/ From owner-chemistry@ccl.net Tue Aug 26 11:43:00 2008 From: "Jerome Kieffer jerome.Kieffer(!)terre-adelie.org" To: CCL Subject: CCL: how to do a biexponential fitting Message-Id: <-37628-080826110205-18083-DPZiv7JIofsr63Ied2eyNQ]_[server.ccl.net> X-Original-From: Jerome Kieffer Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-15 Date: Tue, 26 Aug 2008 16:04:29 +0200 Mime-Version: 1.0 Sent to CCL by: Jerome Kieffer [jerome.Kieffer/./terre-adelie.org] On Tue, 19 Aug 2008 10:16:35 -0400 "arix ahmad nriza_-_hotmail.com" wrote: >=20 > Sent to CCL by: "arix ahmad" [nriza!A!hotmail.com] > Hi All, > Could anyone helps me on fitting a correlation functions curves by biexpo= nential? perhaps using grace or other software. And also could anyone expla= in tu me how to integrate the correlation functions curve to get the correl= ation times? try fityk=20 http://sourceforge.net/projects/fityk --=20 J=E9r=F4me KIEFFER : http://www.terre-adelie.org From owner-chemistry@ccl.net Tue Aug 26 12:17:01 2008 From: "Conley, Michael mconley : leadscope.com" To: CCL Subject: CCL: FDA QSAR Toxicity Models Now Available Message-Id: <-37629-080826114712-11298-6osOIYks6qFdJ0ALuMpjXQ-$-server.ccl.net> X-Original-From: "Conley, Michael" Content-class: urn:content-classes:message Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C90792.F983CC6B" Date: Tue, 26 Aug 2008 11:46:58 -0400 MIME-Version: 1.0 Sent to CCL by: "Conley, Michael" [mconley(~)leadscope.com] This is a multi-part message in MIME format. ------_=_NextPart_001_01C90792.F983CC6B Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: base64 Q29sdW1idXMsIE9oaW8gQXVndXN0IDI2LCAyMDA4IOKAkyBMZWFkc2NvcGUgYW5ub3VuY2VzIHRo 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Mi4wcHQnPkNvbHVtYnVzPC9zcGFuPjwvZm9udD4sIE9oaW8gNDMyMTU8L3A+DQoNCjxwIGNsYXNz PU1zb05vcm1hbD48Zm9udCBzaXplPTMgZmFjZT0iVGltZXMgTmV3IFJvbWFuIj48c3BhbiBzdHls ZT0nZm9udC1zaXplOg0KMTIuMHB0Jz5QaG9uZTogNjE0LTU5OS0yNzAwPC9zcGFuPjwvZm9udD48 L3A+DQoNCjxwIGNsYXNzPU1zb05vcm1hbD48Zm9udCBzaXplPTMgZmFjZT0iVGltZXMgTmV3IFJv bWFuIj48c3BhbiBzdHlsZT0nZm9udC1zaXplOg0KMTIuMHB0Jz5GYXg6Jm5ic3A7IDYxNC02NzUt MzczMjwvc3Bhbj48L2ZvbnQ+PC9wPg0KDQo8cCBjbGFzcz1Nc29Ob3JtYWw+PGZvbnQgc2l6ZT0y IGNvbG9yPW5hdnkgZmFjZT1BcmlhbD48c3BhbiBzdHlsZT0nZm9udC1zaXplOg0KMTAuMHB0O2Zv bnQtZmFtaWx5OkFyaWFsO2NvbG9yOm5hdnknPjxhIGhyZWY9Im1haWx0bzppbmZvQGxlYWRzY29w ZS5jb20iPmluZm9AbGVhZHNjb3BlLmNvbTwvYT4NCjwvc3Bhbj48L2ZvbnQ+PC9wPg0KDQo8cCBj bGFzcz1Nc29Ob3JtYWw+PGZvbnQgc2l6ZT0zIGZhY2U9IlRpbWVzIE5ldyBSb21hbiI+PHNwYW4g c3R5bGU9J2ZvbnQtc2l6ZToNCjEyLjBwdCc+Jm5ic3A7PC9zcGFuPjwvZm9udD48L3A+DQoNCjwv ZGl2Pg0KDQo8L2JvZHk+DQoNCjwvaHRtbD4NCg== ------_=_NextPart_001_01C90792.F983CC6B-- From owner-chemistry@ccl.net Tue Aug 26 12:52:01 2008 From: "Oscar U Ojeda Oscar.Ojeda#%#chemail.tamu.edu" To: CCL Subject: CCL:G: Stress calculations in DFT Message-Id: <-37630-080826105259-15954-CuJM+HwfM+yd6RTBe9zwRQ..server.ccl.net> X-Original-From: "Oscar U Ojeda" Date: Tue, 26 Aug 2008 10:52:55 -0400 Sent to CCL by: "Oscar U Ojeda" [Oscar.Ojeda[]chemail.tamu.edu] Dear CCLr's I would like to inquire if anybody knows how to properly calculate stresses in periodic boundary condition codes; I have found that most planewave codes do this rather easily, while Gaussian-type-orbital codes never report the total stress in a calculation. Most people mention Pulay stresses as the main source of headache. Any kind pointer to a particularly digestible reference is highly appreciated. Best Oscar From owner-chemistry@ccl.net Tue Aug 26 13:31:01 2008 From: "John McKelvey jmmckel===gmail.com" To: CCL Subject: CCL:G: End of a frequency job Message-Id: <-37631-080826122438-5514-O94Snn+rO+ShSnqXfe7hxQ~!~server.ccl.net> X-Original-From: "John McKelvey" Content-Type: multipart/alternative; boundary="----=_Part_12195_30441793.1219758501714" Date: Tue, 26 Aug 2008 09:48:21 -0400 MIME-Version: 1.0 Sent to CCL by: "John McKelvey" [jmmckel===gmail.com] ------=_Part_12195_30441793.1219758501714 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline I have now lost track of why this discussion started, but I completely agree with the statements that it is quite dangerous to do geoms with one basis set and freqs with a different one using the geoms from the previous basis set. It seems quite tenuous at best that if different basis sets give the same geom then the freqs and normal modes will be the same. Practically and pragmatically it seems to have worked in the past that if the basis set for geometry optimization and energy evaluation were done with a basis set too large to be practical for freq calcs then one used a smaller basis set to reopt the geom and scale the associated freqs. Guess it depends on what one is trying to accomplish... John McKelvey On Mon, Aug 25, 2008 at 2:48 PM, Pascal Boulet pascal.boulet# univ-provence.fr wrote: > hello, > > It sounds strange to me that some people are using different basis sets for > optimization and frequency calculations. In principle, the geometry is no > longer at the minimum of the PES when the BS is changed, and in the case of > frequency jobs, one can get imaginary frequencies. > > Pascal > > Close, David M. CLOSED^mail.etsu.edu wrote: > > Sent to CCL by: "Close, David M." [CLOSED__mail.etsu.edu] > Yes, that is exactly right. As a check you could try a frequency calc. > using the same basis set. Usually 3 out of 4 of the "yes" are ok. For > some reason the third "yes" is sometimes a "no". I don't know why. > Now a more basic question. If you are taking a course on doing > calculations, you are always told you must use the same basis sets in > frequency calculations as on the original optimizations. But people > seem to be getting away from this are very large calculations. If it > takes a week to do an optimization, it might take 3-4 weeks to do a > frequency calculation. So people are now using smaller basis sets to do > faster frequency calcs. I do not happen to know if this leads to > problems. I do know that Berny Schlegel warned about this some time > ago, but I do not know the current thinking on this. > > > -----Original Message----- > > > From: owner-chemistry ~~ ccl.net [mailto:owner-chemistry ~~ ccl.net] > > > Sent: Monday, August 25, 2008 11:29 AM > To: Close, David M. > Subject: CCL:G: End of a frequency job > > > Sent to CCL by: Orlin Blajiev [Orlin.Blajiev,vub.ac.be] > David, Alcides, > > > > Thanks for the info. I guess G03 reports the geometry as non-converged > > because I use different BS in Opt and Freq. > > Best regards, > Orlin > > > Alcides Simao alsimao[#]gmail.com wrote: > > > Orlin: > > This is a routine check from GAUSSIAN, made after *all* frequency > jobs. You can safely discart it. Gaussian will always do that, even if > > > you don't flag the 'OPT' option. > > Best, > > Alcides > > > > -- > Dr. Pascal Boulet, Computational Chemist > University of Provence > Laboratoire Chimie Provence, UMR6264 > Centre Saint-Jerome, case MADIREL > F-13397 MARSEILLE Cedex 20, France > Tel. +33 (0) 491 63 71 17 Fax. +33 (0) 491 63 71 11 > courriel: pascal.boulet[]univ-provence.fr http://www.lc-provence.frhttp://allos.up.univ-mrs.fr/boulet > > ------=_Part_12195_30441793.1219758501714 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline
I have now lost track of why this discussion started, but I completely agree with the statements that it is quite dangerous to do geoms with one basis set and freqs with a different one using the geoms from the previous basis set.  It seems quite tenuous at best that if different basis sets give the same geom then the freqs and normal modes will be the same.

Practically and pragmatically it seems to have worked in the past that if the basis set for geometry optimization and energy evaluation were done with a basis set too large to be practical for freq calcs then one used a smaller basis set to reopt the geom and scale the associated freqs.

Guess it depends on what one is trying to accomplish...

John McKelvey

 
On Mon, Aug 25, 2008 at 2:48 PM, Pascal Boulet pascal.boulet#univ-provence.fr <owner-chemistry*o*ccl.net> wrote:
hello,

It sounds strange to me that some people are using different basis sets for optimization and frequency calculations. In principle, the geometry is no longer at the minimum of the PES when the BS is changed, and in the case of frequency jobs, one can get imaginary frequencies.

Pascal

Close, David M. CLOSED^mail.etsu.edu wrote:
Sent to CCL by: "Close, David M." [CLOSED__mail.etsu.edu]
Yes, that is exactly right.  As a check you could try a frequency calc.
using the same basis set.  Usually 3 out of 4 of the "yes" are ok.  For
some reason the third "yes" is sometimes a "no".  I don't know why.
Now a more basic question.  If you are taking a course on doing
calculations, you are always told you must use the same basis sets in
frequency calculations as on the original optimizations.  But people
seem to be getting away from this are very large calculations.  If it
takes a week to do an optimization, it might take 3-4 weeks to do a
frequency calculation.  So people are now using smaller basis sets to do
faster frequency calcs.  I do not happen to know if this leads to
problems.  I do know that Berny Schlegel warned about this some time
ago, but I do not know the current thinking on this.


-----Original Message-----
  
From: owner-chemistry ~~ ccl.net [mailto:owner-chemistry ~~ ccl.net] 
    
Sent: Monday, August 25, 2008 11:29 AM
To: Close, David M.
Subject: CCL:G: End of a frequency job


Sent to CCL by: Orlin Blajiev [Orlin.Blajiev,vub.ac.be]
David, Alcides,



Thanks for the info. I guess  G03 reports the geometry as  non-converged

because I use different  BS in Opt and  Freq.

Best regards,
Orlin


Alcides Simao alsimao[#]gmail.com wrote:
  
Orlin:

This is a routine check from GAUSSIAN, made after *all* frequency 
jobs. You can safely discart it. Gaussian will always do that, even if
    
  
you don't flag the 'OPT' option.

Best,

Alcides
    
  

-- 
Dr. Pascal Boulet, Computational Chemist
University of Provence
Laboratoire Chimie Provence, UMR6264
Centre Saint-Jerome, case MADIREL
F-13397 MARSEILLE Cedex 20, France
Tel. +33 (0) 491 63 71 17 Fax. +33 (0) 491 63 71 11
courriel: pascal.boulet[]univ-provence.fr
http://www.lc-provence.fr
http://allos.up.univ-mrs.fr/boulet

------=_Part_12195_30441793.1219758501714-- From owner-chemistry@ccl.net Tue Aug 26 14:02:00 2008 From: "Yuanyuan Cui wicky.cc * gmail.com" To: CCL Subject: CCL:G: ONIOM calculation errors. Help! Message-Id: <-37632-080826125009-26147-Z14ZLPry3+EE7fzEMGp6rw-*-server.ccl.net> X-Original-From: "Yuanyuan Cui" Date: Tue, 26 Aug 2008 12:50:05 -0400 Sent to CCL by: "Yuanyuan Cui" [wicky.cc*gmail.com] I'm doing a 2-layer ONIOM calculation. My ligand are two Zinc ions are set to the high layer (rhf/6-31g*) and 16 residues from the protein active site around this ligand are set to low layer (i tried amber and am1). I deleted the backbone of the residues and added H for the valence. But I met several problems with this setting. 1. I used gaussview3 to prepare the input file for ONIOM. It works ok for the high layer, but after I set the charge for the low layer to be -2 (two Asp in the low layer), it can't let me to set the multiplicity to be 1 (it only provides the options of 2, 4, etc). This happens for both amber and am1. If I change the multiplicity to be 1 manually in the gaussian input file it generated, it will complain can't combine multiplicity 1 with 258 electrons. What could be the problem of this? 2. When I tried to run with multiplicity to be 2 and use am1 for the low layer, it ran for about one day and got error complaining "unable to achieve self-consistence". I have used SCF(maxcycle=2000). How can I solve this problem? 3. When I tried to run low layer using amber, it keeps complaining "Missing atomic parameters for atom 204". How can I know what parameters it missing and how can I add those parameters? I really appreciate your help! Yuanyuan Cui wicky.cc|-|gmail.com Cambridge, MA USA From owner-chemistry@ccl.net Tue Aug 26 14:37:00 2008 From: "Aleksey Kuznetsov AlexKuznetsov2007-*-yandex.ru" To: CCL Subject: CCL: parallel batch jobs for TM5.10 with the Maui TORQUE scheduler - run failure Message-Id: <-37633-080826141637-24073-4Rv8/p1PN7vBl3MeU3w+/A=-=server.ccl.net> X-Original-From: Aleksey Kuznetsov Content-Transfer-Encoding: 7bit Content-Type: text/plain Date: Tue, 26 Aug 2008 21:44:29 +0400 MIME-Version: 1.0 Sent to CCL by: Aleksey Kuznetsov [AlexKuznetsov2007,+,yandex.ru] Dear CCL Users, We are testing parallel batch jobs for TM5.10 with the Maui TORQUE scheduler and running into problems. Here is one example of a failed job with the following error in the outfile: --------------------------------------------------------------------------------------------------- STARTING ridft ON 3 PROCESSORS! RUNNING PROGRAM /libs/TURBOMOLE_5.10/bin/x86_64-unknown-linux-gnu_mpi/ridft_mpi. PLEASE WAIT UNTIL ridft HAS FINISHED. Look for the output in slave1.output. MACHINEFILE is /var/torque/aux//7145 No file slave1.output found? --------------------------------------------------------------------------------------------------- The SDERR file contains MPI Application rank 0 exited before MPI_Finalize() with status 16 We suppose it can be related to the way TORQUE assigns "nodefile" or "machinefile", but we are not sure. Is anyone familiar with such kind of problems? Any help and advice will be greatly appreciated. Thanks in advance, Aleksey. ------------------------------------------- Dr. Aleksey Kuznetsov Cherry L. Emerson Center for Scientific Computation Emory University 1515 Dickey Drive Atlanta, GA 30322 USA Phone: (404)727-2381 Email: akuznets=euch4e.chem.emory.edu ------------------------------------------- From owner-chemistry@ccl.net Tue Aug 26 15:17:01 2008 From: "Petra Imhof Petra.Imhof]_[iwr.uni-heidelberg.de" To: CCL Subject: CCL: Workshop Methods of Molecular Simulations MMS08 in Heidelberg Oct 7-10 (fwd) Message-Id: <-37634-080826144101-10621-Jw17QOU1RiSfNmdS5aG23w#server.ccl.net> X-Original-From: Petra Imhof Content-ID: Content-Type: MULTIPART/Mixed; BOUNDARY="-830399112-386301551-1218734577=:3189" Date: Tue, 26 Aug 2008 19:49:43 +0200 (CEST) MIME-Version: 1.0 Sent to CCL by: Petra Imhof [Petra.Imhof!^!iwr.uni-heidelberg.de] This message is in MIME format. The first part should be readable text, while the remaining parts are likely unreadable without MIME-aware tools. ---830399112-386301551-1218734577=:3189 Content-Type: TEXT/PLAIN; CHARSET=ISO-8859-1; FORMAT=flowed Content-Transfer-Encoding: 8BIT Content-ID: Dear colleagues, it is my pleasure to announce this year's Workshop "Methods of Molecular Simulations MMS08" in Heidelberg. The objective of the workshop is to report on new developments in the field of methods for molecular simulation, including the topics: * Network-based and Markov state models * Statistical Mechanics * Quantum and Quantum-Classical Methods * Multi-Scale and Coarse-Graining Methods * Protein Folding and Conformational Rearrangement For more information and registration have a look at the web page http://spider.iwr.uni-heidelberg.de/~mms/ Please excuse multiple postings. The organising comittee Petra Imhof J�rg Langowski Jan-Hendrik Prinz ---830399112-386301551-1218734577=:3189-- From owner-chemistry@ccl.net Tue Aug 26 15:52:01 2008 From: "amine amine m-22=-=hotmail.fr" To: CCL Subject: CCL: recompile bondtype Message-Id: <-37635-080826154607-9907-8y1/taWEwLu+kXS5+pwLug]*[server.ccl.net> X-Original-From: "amine amine" Date: Tue, 26 Aug 2008 15:46:03 -0400 Sent to CCL by: "amine amine" [m-22]|[hotmail.fr] Hi I recive this error message antechamber -i ~/xxx.pdb -fi mol2 -o ~/xxxx.prepi -fo prepi -c bcc -j5 Warning: the assigned bond types may be wrong, please : (1) double check the structure (the connectivity) and/or (2) adjust atom valence penalty parameters in APS.DAT, and/or (3) increase PSCUTOFF in define.h and recompile bondtype.c Be cautious, use a large value of PSCUTOFF (>100) will significantly increase the computation time Error: cannot run "AMBERHOME/bin/bondtype -j full -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac" in judgebondtype() of antechamber.c properly, exit From owner-chemistry@ccl.net Tue Aug 26 23:03:00 2008 From: "Brian Salter-Duke brian.james.duke-$-gmail.com" To: CCL Subject: CCL: End of a frequency job Message-Id: <-37636-080826221931-5719-augKbjXCFJhTQ+v9Myo+Jw(!)server.ccl.net> X-Original-From: Brian Salter-Duke Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 27 Aug 2008 11:48:35 +1000 MIME-Version: 1.0 Sent to CCL by: Brian Salter-Duke [brian.james.duke- -gmail.com] Toomas Tamm tt-ccl2a/yki.ttu.ee wrote: > Sent to CCL by: Toomas Tamm [tt-ccl2=yki.ttu.ee] > On Mon, 2008-08-25 at 13:46 -0400, Close, David M. CLOSED^mail.etsu.edu > wrote: > >> Now a more basic question. If you are taking a course on doing >> calculations, you are always told you must use the same basis sets in >> frequency calculations as on the original optimizations. But people >> seem to be getting away from this are very large calculations. If it >> takes a week to do an optimization, it might take 3-4 weeks to do a >> frequency calculation. So people are now using smaller basis sets to do >> faster frequency calcs. > > On several occasions, we have re-optimized the structure with a smaller > basis set, checked that no significant changes in geometry have occurred > (usually the gradients at initial optimization step, and the number of > additional steps needed, are good diagnostics, too), and then performed > a frequency calculation for the re-optimized geometry, using the smaller > basis set. We have even used the zero-point energies from such > calculations together with electronic energies from the large-basis > calculations. > > I believe this is theoretically correct, just less accurate than > calculating the frequencies with the larger basis set. Of course there > remains the slight possiblity that the large-basis-set geometry was a > transition state while the small-basis-set geometry is a minimum. We > have considered the risk small enough given the savings in computation > time. > > Any comments on this procedure? That is fine. Using a lower level of the theory for the ZPE correction is OK. It is done in the G2 and G3 methods for example. It calculates frequencies at the stationary point for the basis set and method being used. What is incorrect is calculating a frequency at a stationary point > from an different level of theory. Brian. -- Brian Salter-Duke (Brian Duke) Brian.James.Duke _ gmail.com Post: 626 Melbourne Rd, Spotswood, VIC, 3015, Australia http://www.salter-duke.bigpondhosting.com/brian/index.htm Honorary Researcher Fellow, Monash Institute of Pharmaceutical Sciences