From owner-chemistry@ccl.net Tue Jun 7 00:06:00 2011 From: "Ajitha Manjaly John aji.john07-x-gmail.com" To: CCL Subject: CCL: effect of temperature and pressure in a reaction step Message-Id: <-44854-110607000314-18193-6zhaOP6jbg/PL3KtBdsqUg(-)server.ccl.net> X-Original-From: "Ajitha Manjaly John" Date: Tue, 7 Jun 2011 00:03:13 -0400 Sent to CCL by: "Ajitha Manjaly John" [aji.john07|*|gmail.com] Hello CCL users,, It will be very grateful if I know the best possible method to include the effect of pressure (for eg. nitrogen atmosphere at 4 Mpa) and temperature for calculating a reaction step (including transition state) by using density functional theory.... Is there any other useful route?? Thanks in advance, AMJ From owner-chemistry@ccl.net Tue Jun 7 08:56:00 2011 From: "=?UTF-8?B?546L5bu6QWJib3R0IFdBTkc=?= abbott.cn],[gmail.com" To: CCL Subject: CCL:G: How to build a linux cluster for computational chemistry purposes?, HELP Message-Id: <-44855-110607003744-12518-Uc3SV6Ky311L5FRce+lt5A#server.ccl.net> X-Original-From: =?UTF-8?B?546L5bu6QWJib3R0IFdBTkc=?= Content-Type: multipart/alternative; boundary=bcaec520ec21f4565704a517c65f Date: Tue, 7 Jun 2011 12:37:27 +0800 MIME-Version: 1.0 Sent to CCL by: =?UTF-8?B?546L5bu6QWJib3R0IFdBTkc=?= [abbott.cn**gmail.com] --bcaec520ec21f4565704a517c65f Content-Type: text/plain; charset=UTF-8 A cluster for G03 is quite simple. I have done this on both Debian and RHEL based OS. First of all, Link all the nodes physically. Then, A, configure all the nodes (master and slave with the SAME OS installation and application installation.) or, B, configure the master node only, put all the file (eps. G03 installation in a share directory). In this case, you need configure NFS on master server, NFS client on all nodes. The configuration of NFS server and client is quite easy, you can google it for detail. Step 3. Configure passwdless login. A, use NIS to do this. or, B, configure ssh passwdless login I prefer solution B. ------------------------------------------ For more info, contact me via email. Good luck. ^_^ * **Abbott WANG* State Key Lab of Theoretical & Computational Chemistry Institute of Theoretical Chemistry Jilin University Changchun, 130023 P.R. China Tel.+86-135-9617-5450 Email: abbott.cn~~gmail.com On Tue, Jun 7, 2011 at 2:20 AM, Miguel Quiliano Meza rifaximina!A!gmail.com wrote: > Hi Jun. > > Excellent, as you can understand... I will be waiting..!! impatienly. > > Of course, I going to share with you all my "mistakes" during my > experience. > > Best regards. > > Miguel Quiliano > > > 2011/6/4 Jun Zhang coolrainbowa/yahoo.cn > >> Hello Karen: >> >> Thank you for your suggestions. >> >> The document is in fact a summary of my early works (2009~2010) when I >> started to build clusters for my lab. After the cluster being stable and >> relatively good efficiency, I began to work in computational chemistry and >> some programming, seldomly trying new techniques in clusters (such as Rocks, >> Lustre, Slurm, etc). >> >> Since I am far from an "expert" in cluster building, my document has to >> wait for a long time before publishing until its author becoming more >> "professional" in the field. Just a joke. If the needs are really high, I >> will try to put it into English and be very happy to share it . >> >> Cheers up! >> >> Jun Zhang >> Nankai University >> coolrainbow..yahoo.cn >> >> --- *Karen.Green..sanofi-aventis.com * >> >> >> Karen.Green..sanofi-aventis.com Karen.Green..sanofi-aventis.com >> RE: G: How to build a linux cluster for computational chemistry >> purposes?, HELP >> coolrainbow..yahoo.cn >> >> Dear Jun, >> >> Have you ever considered translating it into English and publishing with a >> technical/scientific publisher like McGraw-Hill? >> (It seems that your hard work could benefit others and also maybe yourself >> financially.) >> >> I recall in the past that a professor of mine had designed a course for >> upper-level undergraduates that had no textbook because he said that none >> addressed his needs. >> I asked him why he didn't publish it since he had already done the work. >> Now that book is a classic medicinal chemistry textbook (The Organic >> Chemistry of Drug Design and Drug Action). >> >> I get the same feeling about your work referenced in your email. >> >> Just a thought (although I am not a publisher but a fellow research >> scientist), >> Karen >> >> ------------------------------ >> *From:* owner-chemistry+karen.green==sanofi-aventis.com..ccl.net [mailto: >> owner-chemistry+karen.green==sanofi-aventis.com..ccl.net] *On Behalf Of *Jun >> Zhang coolrainbow]*[yahoo.cn >> *Sent:* Thursday, June 02, 2011 7:31 PM >> *To:* Green, Karen R&D/US >> >> *Subject:* CCL:G: How to build a linux cluster for computational >> chemistry purposes?, HELP >> >> Hi Miguel Quiliano: >> >> I had ever written a very detailed document on cluster building, but >> it was written in Chinese rather than in English so I don't know whether it >> can help you... If you need it, I can send you by e-mail. >> >> Good Luck! >> >> Jun Zhang >> Nankai University >> coolrainbow(_)yahoo.cn >> >> >> Dear community. >> >> After... talk.. and talk.. with my boss, I convinced him to build a linux >> cluster for computational chemistry purposes, in other words... to use >> Gaussian03. So now I have 80 cores at my disposal. We also have >> TCP/LINDA. >> >> Could you please recommend me, one operative system and some online guide >> to build it or book? Personal experiences are welcome. >> >> Thanks in advance. >> >> Miguel Quiliano. >> >> > --bcaec520ec21f4565704a517c65f Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable A cluster for G03 is quite simple.=C2=A0

I have done thi= s on both Debian and RHEL based OS.=C2=A0

First of= all,=C2=A0
Link all the nodes physically.

Then,=C2=A0
A, configure all the nodes (master and slave with the SAME OS installa= tion and application installation.)
or,=C2=A0
B, config= ure the master node only, put all the file (eps. G03 installation in a shar= e directory).=C2=A0
In this case, you need configure NFS on master server, NFS client on a= ll nodes.=C2=A0
The configuration of NFS server and client is qui= te easy, you can google it for detail.=C2=A0

Step = 3.=C2=A0
Configure passwdless login.=C2=A0
A, use NIS to do this.=C2= =A0
or,
B, configure ssh passwdless login
I p= refer solution B.=C2=A0



<= div>------------------------------------------
For more info,=C2=A0
contact me via email.=C2=A0
<= br>
Good luck.=C2=A0

^_^



Abbott WANG
State Key Lab of Theoretical &a= mp; Computational Chemistry
Institute of Theoretical Chemistry
Jilin University
Changchun, 130023=
P.R. China
Tel.+86-135-9617-5450
Email:=C2=A0abbott.= cn~~gmail.com





On Tue, Jun 7, 2011 at 2:20 AM, Miguel Q= uiliano Meza rifaximina!A!gmail.com <owner-chemistry[A]= ccl.net> wrote:
Hi Jun.

Excellent, as you can unders= tand... I will be waiting..!! impatienly.

Of course, I going to shar= e with you all my "mistakes" during my experience.

Best regards.

Miguel Quiliano


2011/6/4 Jun Zhang coolrainbowa/yahoo.cn <<= a href=3D"mailto:owner-chemistry%7B%7Dccl.net" target=3D"_blank">owner-chem= istry{}ccl.net>
Hello=C2=A0 Karen:
=C2=A0
Thank you for your suggestions.
=C2=A0
The document is in fact a summary of my early works (2009~2010) when I= started to build clusters for my lab. After the cluster being stable and r= elatively=C2=A0good efficiency, I began to work in computational chemistry = and some programming, seldomly trying new techniques in clusters (such as R= ocks, Lustre, Slurm, etc).
=C2=A0
Since I am far from an "expert" in cluster building, my=C2= =A0document has to wait for a long time before publishing until its author = becoming more "professional" in the fiel= d. Just a joke. If the needs=C2=A0are really high, I will try to put it int= o English and be very happy to share it .
=C2=A0
Cheers up!

Jun Zhang
Nankai University
coolrainbow..yahoo.cn

--- Karen.Green..san= ofi-aventis.com <Karen.Green..sanofi-aventis.com>

=C2=A0Karen.Green..sanofi-aventis.com Karen.Green..sanofi-av= entis.com
=C2=A0RE: G: How to build a linux cluster for computational chemistry purpo= ses?, HELP
=C2=A0coolrainbow..yahoo.cn

Dear Jun,
=C2=A0
Have you ever considered translating it into English and publi= shing with a technical/scientific publisher like McGraw-Hill?=
(It seems that your hard work could benefit others and also ma= ybe yourself financially.)
=C2=A0
I recall in the past that a professor of mine had designed a c= ourse for upper-level undergraduates that had no textbook because he said t= hat none addressed his needs.
I asked him why he didn't publish it since he had already = done the work.=C2=A0 Now that book is a classic medicinal chemistry textboo= k (The Organic Che= mistry of Drug Design and Drug Action).
=C2=A0
I get the same feeling about your work referenced in your emai= l.
=C2=A0
Just a thought= (although I am not a publisher but a fellow research scientist),
Karen

From: owner-chemistry+karen.green= =3D=3Dsanofi-aventi= s.com..ccl.net [mailto= :owner-c= hemistry+karen.green=3D=3Dsanofi-aventis.com..ccl.net] On Behalf Of Jun Zhang coolrainbow]*[yahoo.cn
Sent: Thursday, June 02, 2011 7:31 PM
To: Green, Karen R&a= mp;D/US

Subject: CCL:G: How to build a linux cluster for com= putational chemistry purposes?, HELP

Hi Miguel Quiliano:
=C2=A0
=C2=A0=C2=A0=C2=A0=C2=A0 I had ever written a very detailed document= =C2=A0on cluster building, but it was written in Chinese rather than=C2=A0i= n English so I don't know whether it can help you... If you need it, I = can send you by e-mail.
=C2=A0
Good Luck!

Jun Zhang
Nankai University
coolrainbow(_)yahoo.cn


Dear community.

After... talk.. and talk.. with my boss, I convinced him to build a linux cluster f= or computational chemistry purposes, in other words... to use Gaussian03. <= /span>So now I have 80 cores at my disposal. We also have TCP/LINDA.

Could you please recommend me, one operative system and some online gui= de to build it or book? Personal experiences are welcome.

Thanks in = advance.

Miguel Quiliano.


--bcaec520ec21f4565704a517c65f-- From owner-chemistry@ccl.net Tue Jun 7 09:31:00 2011 From: "Nuno A. G. Bandeira nuno.bandeira,ist.utl.pt" To: CCL Subject: CCL:G: CMO-NICS with NBO 5.G Message-Id: <-44856-110607083042-13936-1J0ATu9zCQCMGWp+EdaQ+g~!~server.ccl.net> X-Original-From: "Nuno A. G. Bandeira" Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 07 Jun 2011 14:30:12 +0200 MIME-Version: 1.0 Sent to CCL by: "Nuno A. G. Bandeira" [nuno.bandeira]-[ist.utl.pt] In 2009 someone enquired on this list about an error message in NBO 5.G relating to the computation of CMO-NICS values i.e. NICS values dissected per MO. At the time when we published our paper in 2007 (Struct. Chem., 18 (2007) 841-847) we used a combination of NBO 5.0 and a late version of Gaussian 98 with this link 607 recompiled. It seems that with NBO 5.G there's an internal check for the basis set of every atom including ghosts that make the program spit out an error message like this: «Subroutine NAOANL could not find a s-type valence orbital on atom gh 13. IVAL : 1 0 0 0 M : 1 LA : 1 Missing valence orbital in SR NAOANL. » or this: « The gh basis set should include 1 s-type subshell(s); 0 found. Error: NBHALT Error termination via Lnk1e in /home/nuno/g03/l607.exe at Thu Jun 2 19:35:46 2011. » I've since received a few emails about this but since I had moved on to other things I could not look into what was the source of the problem. Now that I'm back to recomputing NICS values for other interesting compounds I got round to the source of the problem. The solution unfortunately requires tampering with the source code of NBO 5.G and recompiling link607. Here's how you should do it: 1) comment out the following lines (8382-8397) : C Ensure that a sufficient number of subshells exists: C C (Exception: La may be missing a valence f subshell.) C C IF(IL.LT.5) THEN C IF(NL.LT.ICORE(IL)+IVAL(IL)) THEN C IF(IATNO(ICNTR).EQ.57.AND.IL.EQ.4) THEN C WRITE(LFNPR,910) C CALL VALTBL(ICNTR,IVAL,-4) C ELSE C WRITE(LFNPR,920) CHARAT(IATNO(ICNTR)), C + ICORE(IL)+IVAL(IL),STR(IL),NL C CALL NBHALT(' ') C END IF C END IF C END IF 2) Also comment out these which turn up more than once (line 8812 and 15835) : C IF(MORB.EQ.0) THEN C WRITE(LFNPR,2600) ITYP,NAMEAT(IATNO(NCTR)),NCTR, C + (IVAL(I),I=1,4),M,LA C CALL NBHALT('Missing valence orbital in SR NAOANL.') C END IF 3) Recompile link 607 as stated in prof. Weinhold's site http://www.chem.wisc.edu/~nbo5/install.txt and you should be ready to go. Best wishes, -- Nuno A. G. Bandeira, AMRSC Departamento de Química Física i Inorgánica Despatx 207, N4 - Universitat Rovira i Virgili Campus Sescelades, Carrer Marcel.lí Domingo 43007 Tarragona - SPAIN -- From owner-chemistry@ccl.net Tue Jun 7 12:55:00 2011 From: "Lars Goerigk lars.goerigk() uni-muenster.de" To: CCL Subject: CCL:G: Information about the TD-B2PLYP method ... Message-Id: <-44857-110607090052-16657-763Fwc+5a3NIk5Ahf+FWzQ,+,server.ccl.net> X-Original-From: Lars Goerigk Content-Transfer-Encoding: 8bit Content-Type: Text/Plain; charset="iso-8859-1" Date: Tue, 7 Jun 2011 15:00:41 +0200 MIME-Version: 1.0 Sent to CCL by: Lars Goerigk [lars.goerigk : uni-muenster.de] Dear CCL-subscribers, I'd like to use this mailing-list to clarify an important point regarding the TD-B2PLYP method for excited state problems. This approach was originally published by Grimme and Neese ( J. Chem. Phys. 2007, 127, 154116) and later several times successfully applied by the Grimme group. Recently, also other groups published results based on TD-B2PLYP, but in some cases I became aware of a possible misunderstanding, which I would like to clarify here. Double-hybrids, like B2PLYP, consist of two parts, a hybrid-GGA portion and an additional perturbative correlation contribution. In the first TD-B2PLYP publication, the authors explain that first a standard linear response TD-DFT treatment for the hybrid-GGA part of the functional is carried out. This hybrid portion of B2PLYP is often also called B2LYP. These resulting TD-B2LYP excitation energies and the B2LYP ground state orbitals are then used for a CIS(D) type perturbative treatment. This perturbative correction is then added to the TD-B2LYP energies and one obtains the final TD-B2PLYP values. Please note that the additional CIS(D) type calculation is crucial!!. Otherwise, one only obtains TD-B2LYP excitation energies, which are practically identical to TD-BHLYP ones. Yesterday, I received an email from the Gaussian Support team, that the TD-B2PLYP method for excited states is not implemented in Gaussian09. Simply stating the b2plyp and the td/rpa keywords in the input section only leads to TD-B2LYP excitation energies!! To the best of my knowledge, ORCA is the only available quantum chemistry package, with which it is possible to carry out B2PLYP treatments for excited state properties. However, note that currently ORCA can only apply the Tamm-Dancoff-Approximation to double-hybrids! Maybe I'm wrong, and already other programs have TD-B2PLYP included. Anyway, my intention was not to suggest a specific program, but I just wanted to make this important point clear. I hope that this hint is appreciated by people who actually consider the application of TD-B2PLYP to their problems. With best wishes, Lars Goerigk -- Dr. Lars Goerigk Theoretical Organic Chemistry Organisch-Chemisches Institut Universität Münster Corrensstrasse 40 48149 Münster Germany From owner-chemistry@ccl.net Tue Jun 7 22:58:00 2011 From: "Abhishek Dutta Chowdhury abhishekdc[]iitb.ac.in" To: CCL Subject: CCL: activation barrier Message-Id: <-44858-110607225657-3349-2kCtl3zRFyLea6Ktvl7A+Q(a)server.ccl.net> X-Original-From: "Abhishek Dutta Chowdhury" Date: Tue, 7 Jun 2011 22:56:56 -0400 Sent to CCL by: "Abhishek Dutta Chowdhury" [abhishekdc(0)iitb.ac.in] Hi ALL: What is the maximum energy limit of activation barrier in any catalytic reaction at RT (at B3LYP level of theory)? Is it can go beyond 30 KCal/mol?? Many thanks in advance. best wishes, Abhishek