From owner-chemistry@ccl.net Sat Dec 17 02:58:00 2005 From: "FyD fyd:u-picardie.fr" To: CCL Subject: CCL:G: OT:Fedora Core 3 or 4 and Gaussian - exec problem Message-Id: <-30348-051217023739-22463-MKOnjLcvikrgO1t75/TkYQ:server.ccl.net> X-Original-From: FyD Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Sat, 17 Dec 2005 08:37:27 +0100 MIME-Version: 1.0 Sent to CCL by: FyD [fyd[]u-picardie.fr] Quoting "Grzegorz Bakalarski grzesb(!)biogeo.uw.edu.pl" : I have the same problems and agree with your conclusions about the kernel in FC. My guess is that it is a kernel problem: Gaussian seems to not work with the default kernel 2.6.11. provided by FC 4.0... I tested the default 2.6.14 updating my FC install: same problem. It does not work. I have a kernel where g98 works (2.6.12.3, that I recompiled): I could send you my .config file which could be a starting point for your hardware if you wish to test different kernel options in your compilations... I was not able to find the problem. Regards, Francois > Sent to CCL by: Grzegorz Bakalarski [grzesb|*|biogeo.uw.edu.pl] > Dear All, > > I'm sorry for slightly off topic and again gaussian query! > > I feel it is rather linux query so more off-topicism and again I'm sorry. > > The situation is a following: > > I have few linux workstations: one with very new SuSE 10.0, > one with Fedora Core 3 and one with Fedora Core 4 (unfortunately > Fedora is not supported by gaussian, but I cannot change > it to SuSE due to other issues). > I have also PGI Fortran compiler v. 6.05. > Also I have source codes for various gaussian relases > (since G98 E.2 up to G03 D.1 - we are on maintenance). > > Compilation on Fedora machines as well as on SuSE machine > goes smoothly without any problems. > > One SuSE machine execution of a test job goes like a charm. > > But on Fedora machines (3 or 4 ) I get an error at a very > begining saying: > > ****************************************** > Gaussian 03: IA32L-G03RevD.01 13-Oct-2005 > 16-Dec-2005 > ****************************************** > %nproc=1 > Will use up to 1 processors via shared memory. > %mem=20mw > Erroneous write during file extend. write 1896 instead of 4096 > Probably out of disk space. > Erroneous write during file extend. write 1896 instead of 4096 > Probably out of disk space. > Write error in NtrExt1 > Write error in NtrExt1: No such file or directory > > Of course the machine has 20GB of disk space and a test job > is HF/3-21G* for water molecule so a diskspace can;t be an issuse. > > What is more strange one of Fedora machines had Fedorea Core 2 (or maybe 1) > previously and g03 C.2 has run on it successfuly. I tried to run this version > of G03 as well as G98 E.2 with exactly the same error message. > > I tried to debug the problem using strace tool and it showed that > whenever G03 (or G98) tried to open internal files like chk, rwf, > int, d2e which were not present (need not to !!!) it created them and > then tried to write to them but the count of written blocks did not match. > Typilac strace output looked like: > > open("/tmp/Gau-5823.scr", O_RDWR|O_LARGEFILE) = -1 ENOENT (No such file or > directory) > open("/tmp/Gau-5823.scr", O_RDWR|O_CREAT|O_TRUNC|O_LARGEFILE, 0666) = 6 > _llseek(6, 0, [0], SEEK_END) = 0 > fstatfs64(6, 84, {f_type="EXT2_SUPER_MAGIC", f_bsize=4096, f_blocks=4923709, > f_bfree=2412286, f_bavail=2162175, f_files=2501856, > f_ffree=2268833, f_fsid={0, 0}, f_namelen=255, f_frsize=4096}) = 0 > _llseek(6, 0, [0], SEEK_END) = 0 > write(6, "\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0"..., 524288) > = 1064 > write(1, "Erroneous write during file exte"..., 91) = 91 > > Resulting file had always size of 4096 bytes (NB correct one!). > > What is really more strange I found a method to run the test job on the > Fedora machines. > On my SuSE machine I've run the test jobs and generated all > internal files using % directives (e.g. added the following lines > to an input file: > > %chk=wat.chk > %rwf=wat.rwf > %scr=wat.scr > %d2e=wat.d2e > %int=wat.int > > ) > Then I copied the files to Fedora machine and also modified > input file. > The I've run g03 again and it did the jobs very well ... > > I guess there have to be some problem with Fedora config or kernel > settings ..... > A system admin of the machine said it is purely vanilla > installation without any security (SE) settings. > I'm not sysadmin and have little knowledge on Fedora linux > so I ask you for help .. > > Thanks for any friendly suggestion! > > GB> > > > -- * F.-Y. Dupradeau * DMAG EA 3901 & Faculte de Pharmacie, Amiens, France **** http://www.u-picardie.fr/labo/lbpd/FyD.htm From owner-chemistry@ccl.net Sat Dec 17 11:52:00 2005 From: "Jinming zhou fit_tone,yahoo.com" To: CCL Subject: CCL: Force feild of cyclic oligosaccharides Message-Id: <-30349-051217041007-26416-OPYBOhNxxiooABKVUCTQww|server.ccl.net> X-Original-From: Jinming zhou Content-Transfer-Encoding: 8bit Content-Type: multipart/alternative; boundary="0-1623593540-1134806993=:79114" Date: Sat, 17 Dec 2005 00:09:53 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: Jinming zhou [fit_tone- -yahoo.com] --0-1623593540-1134806993=:79114 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit The Glycam FF may do this work, you can have a try. the link: http://glycam.ccrc.uga.edu/AMBER/index.html "sudipta kumar sinha sudiptakumar_sinha|,|yahoo.com" wrote: Sent to CCL by: sudipta kumar sinha [sudiptakumar_sinha#,#yahoo.com] --0-491515816-1134674228=:89029 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Hi everyone , I am sudipta an M.sc. student at IIT-KGP, I am doing my final year project about the dynamics of different non polar solvent around a cyclic oligosaccharides. Could anyone help me to know, how i get the force field of different cyclic oligosaccharides. I will appreaciate your kind help...... sudipta........ --------------------------------- Yahoo! Shopping Find Great Deals on Holiday Gifts at Yahoo! Shopping --0-491515816-1134674228=:89029 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Hi everyone , I am sudipta an M.sc. student at IIT-KGP, I am doing my final year project about the dynamics of different non polar solvent around a cyclic oligosaccharides. Could anyone help me to know, how i get the force field of different cyclic oligosaccharides. I will appreaciate your kind help...... sudipta........ --------------------------------- Yahoo! Shopping Find Great Deals on Holiday Gifts at ">Yahoo! Shopping --0-491515816-1134674228=:89029--http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt-- Jinming Zhou Tel: +86-021-54925277 Email: zhoujm===mail.sioc.ac.cn CCL(Computer Chemstry Lab) Shanghai Institute of Organic Chemistry Chinese Academy of Sciences shanghai 200032 china __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com --0-1623593540-1134806993=:79114 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: 8bit

The Glycam FF may do this work, you can have a try.

the link: http://glycam.ccrc.uga.edu/AMBER/index.html

"sudipta kumar sinha sudiptakumar_sinha|,|yahoo.com" <owner-chemistry===ccl.net> wrote:

Sent to CCL by: sudipta kumar sinha [sudiptakumar_sinha#,#yahoo.com]
--0-491515816-1134674228=:89029
Content-Type: text/plain; charset=iso-8859-1
Content-Transfer-Encoding: 8bit

Hi everyone ,

I am sudipta an M.sc. student at IIT-KGP, I am doing my final year project about the dynamics of different non polar solvent around a cyclic oligosaccharides. Could anyone help me to know, how i get the force field of different cyclic oligosaccharides. I will appreaciate your kind help......

sudipta........

---------------------------------
Yahoo! Shopping
Find Great Deals on Holiday Gifts at Yahoo! Shopping
--0-491515816-1134674228=:89029
Content-Type: text/html; charset=iso-8859-1
Content-Transfer-Encoding: 8bit

Hi everyone ,

I am sudipta an M.sc. student at IIT-KGP, I am doing my final year project about the dynamics of different non polar solvent around a cyclic oligosaccharides. Could anyone help me to know, how i get the force field of different cyclic oligosaccharides. I will appreaciate your kind help......

sudipta........

Yahoo! Shopping

Find Great Deals on Holiday Gifts at Yahoo! Shopping
--0-491515816-1134674228=:89029--

http://www.ccl.net/cgi-bin/ccl/send_ccl_message
http://www.ccl.net/cgi-bin/ccl/send_ccl_message
http://www.ccl.net/chemistry/sub_unsub.shtml
http://www.ccl.net/spammers.txt

--
Jinming Zhou
Tel: +86-021-54925277
Email: zhoujm===mail.sioc.ac.cn
CCL(Computer Chemstry Lab)
Shanghai Institute of Organic Chemistry
Chinese Academy of Sciences
shanghai 200032 china

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http://mail.yahoo.com --0-1623593540-1134806993=:79114-- From owner-chemistry@ccl.net Sat Dec 17 12:27:00 2005 From: "Jinsong Zhao jszhao!^!mail.hzau.edu.cn" To: CCL Subject: CCL: adsorption, ab initio study Message-Id: <-30350-051217091516-20060-R0uJMP4+b0vJ5UAmDkAhgw.:.server.ccl.net> X-Original-From: "Jinsong Zhao" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="iso-8859-1" Date: Sat, 17 Dec 2005 21:39:21 +0800 Mime-Version: 1.0 Sent to CCL by: "Jinsong Zhao" [jszhao[a]mail.hzau.edu.cn] Dear all, I think someone here do researches on adsorption using ab initio method. I hope you would like to point me out how to construct a model that will be suite for computation using ab initio methods. I just know there are two models widely used in adsorption study, one is cluster model, the other is SLAB model. However, I don't know how to construct such model. And what's the suitable program? Any comments, suggestions or tutorials will be really appreciated! Thanks in advance! Jinsong Zhao College of Resources and Environment Huazhong Agricultural University Wuhan 430070, P.R. China E-mail: jszhao]![mail.hzau.edu.cn From owner-chemistry@ccl.net Sat Dec 17 13:02:00 2005 From: "sudip chakraborty sudip_1112000]~[yahoo.com" To: CCL Subject: CCL: Calculate Inherent energy Message-Id: <-30351-051217081039-13637-mMhCc7zLGCfLZ0QczuOQMA.@.server.ccl.net> X-Original-From: sudip chakraborty Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-1 Date: Sat, 17 Dec 2005 04:08:29 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: sudip chakraborty [sudip_1112000() yahoo.com] Hi everyone, Is there any free software or code by which one can generate the Inherent structure of water molecules. I am waiting for yours help. sudip __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com From owner-chemistry@ccl.net Sat Dec 17 13:37:00 2005 From: "Christian Melkonian melkonia===ens-lyon.fr" To: CCL Subject: CCL:G: OT:Fedora Core 3 or 4 and Gaussian - exec problem Message-Id: <-30352-051217055928-20092-gxeahQjuLmkszjMomR8L4A\a/server.ccl.net> X-Original-From: Christian Melkonian Content-Type: TEXT/PLAIN; charset=US-ASCII Date: Sat, 17 Dec 2005 10:58:10 +0100 (CET) MIME-Version: 1.0 Sent to CCL by: Christian Melkonian [melkonia!A!ens-lyon.fr] Hello everybody, A few month ago, I've got the same problem and I've found a temporary solution (but it works...) : > From melkonia|*|ens-lyon.fr Fri Feb 18 10:21:12 2005 +0100 Date: Fri, 18 Feb 2005 10:21:11 +0100 (CET) > From: Christian Melkonian X-X-Sender: To: Bryan Putnam cc: Subject: Re: CCL:g03 on an IA32 platform running RH Enterprise In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Status: O X-Status: X-Keywords: X-UID: 686 Hello, Sorry for my English. I've compiled G03-B.05 with success on a RH Entreprise in a cluster of Athlon with IFC and PGF 5.0. How ? I've just changed the "!=" by "==" in the bsd/mdutil.c (I found this clue with Google, not by Gaussian) where the message appears. Why ? Because the same version on Pentium with Mandrake works very well with IFC. But one consequence is : It's very very slow (???) and sometimes it doesn't work properly... Christian On Thu, 17 Feb 2005, Bryan Putnam wrote: > Dear all, > > I realize that Gaussian, Inc. officially supports only SuSE or Red Hat > Linux on IA32 platforms. However, has anyone had any success in building > an IA32 (i386, 32-bit) version of g03-C.02 (or any earlier version of g03) > on a 32-bit system running Red Hat Enterprise? I was however able to get > an IA64 (AMD64) version to work correctly on an Opteron64 running RHE. > > I was able to get an IA32 version of g03-C.02 to build and run correctly > on a Debian system, but on a RH Enterprise system, we get the error > message: > > Erroneous write during file extend. write -1 instead of 4096 > Probably out of disk space. > Write error in NtrExt1 > > I've tried lots of ideas, using pgi-5.1-4, pgi-5.1-6, pgi-5.2-4, tried > linking statically, turned off optimization, etc., but no success > > Any ideas appreciated! > Thanks, > Bryan > > Bryan F. Putnam > Rosen Center for Advanced Computing > Information Technology at Purdue (ITaP) > Young Hall 519 > Ph 765-496-8225 Fax 765-494-0566 > bfp|*|purdue.edu I hope it can help you. Christian Melkonian On Sat, 17 Dec 2005, FyD fyd:u-picardie.fr wrote: > Sent to CCL by: FyD [fyd[]u-picardie.fr] > Quoting "Grzegorz Bakalarski grzesb(!)biogeo.uw.edu.pl" > : > > I have the same problems and agree with your conclusions about the kernel in FC. > My guess is that it is a kernel problem: > > Gaussian seems to not work with the default kernel 2.6.11. provided by FC 4.0... > I tested the default 2.6.14 updating my FC install: same problem. It does not > work. > > I have a kernel where g98 works (2.6.12.3, that I recompiled): I could send you > my .config file which could be a starting point for your hardware if you wish > to test different kernel options in your compilations... I was not able to find > the problem. > > Regards, Francois > > > > Sent to CCL by: Grzegorz Bakalarski [grzesb|*|biogeo.uw.edu.pl] > > Dear All, > > > > I'm sorry for slightly off topic and again gaussian query! > > > > I feel it is rather linux query so more off-topicism and again I'm sorry. > > > > The situation is a following: > > > > I have few linux workstations: one with very new SuSE 10.0, > > one with Fedora Core 3 and one with Fedora Core 4 (unfortunately > > Fedora is not supported by gaussian, but I cannot change > > it to SuSE due to other issues). > > I have also PGI Fortran compiler v. 6.05. > > Also I have source codes for various gaussian relases > > (since G98 E.2 up to G03 D.1 - we are on maintenance). > > > > Compilation on Fedora machines as well as on SuSE machine > > goes smoothly without any problems. > > > > One SuSE machine execution of a test job goes like a charm. > > > > But on Fedora machines (3 or 4 ) I get an error at a very > > begining saying: > > > > ****************************************** > > Gaussian 03: IA32L-G03RevD.01 13-Oct-2005 > > 16-Dec-2005 > > ****************************************** > > %nproc=1 > > Will use up to 1 processors via shared memory. > > %mem=20mw > > Erroneous write during file extend. write 1896 instead of 4096 > > Probably out of disk space. > > Erroneous write during file extend. write 1896 instead of 4096 > > Probably out of disk space. > > Write error in NtrExt1 > > Write error in NtrExt1: No such file or directory > > > > Of course the machine has 20GB of disk space and a test job > > is HF/3-21G* for water molecule so a diskspace can;t be an issuse. > > > > What is more strange one of Fedora machines had Fedorea Core 2 (or maybe 1) > > previously and g03 C.2 has run on it successfuly. I tried to run this version > > of G03 as well as G98 E.2 with exactly the same error message. > > > > I tried to debug the problem using strace tool and it showed that > > whenever G03 (or G98) tried to open internal files like chk, rwf, > > int, d2e which were not present (need not to !!!) it created them and > > then tried to write to them but the count of written blocks did not match. > > Typilac strace output looked like: > > > > open("/tmp/Gau-5823.scr", O_RDWR|O_LARGEFILE) = -1 ENOENT (No such file or > > directory) > > open("/tmp/Gau-5823.scr", O_RDWR|O_CREAT|O_TRUNC|O_LARGEFILE, 0666) = 6 > > _llseek(6, 0, [0], SEEK_END) = 0 > > fstatfs64(6, 84, {f_type="EXT2_SUPER_MAGIC", f_bsize=4096, f_blocks=4923709, > > f_bfree=2412286, f_bavail=2162175, f_files=2501856, > > f_ffree=2268833, f_fsid={0, 0}, f_namelen=255, f_frsize=4096}) = 0 > > _llseek(6, 0, [0], SEEK_END) = 0 > > write(6, "\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0"..., 524288) > > = 1064 > > write(1, "Erroneous write during file exte"..., 91) = 91 > > > > Resulting file had always size of 4096 bytes (NB correct one!). > > > > What is really more strange I found a method to run the test job on the > > Fedora machines. > > On my SuSE machine I've run the test jobs and generated all > > internal files using % directives (e.g. added the following lines > > to an input file: > > > > %chk=wat.chk > > %rwf=wat.rwf > > %scr=wat.scr > > %d2e=wat.d2e > > %int=wat.int > > > > ) > > Then I copied the files to Fedora machine and also modified > > input file. > > The I've run g03 again and it did the jobs very well ... > > > > I guess there have to be some problem with Fedora config or kernel > > settings ..... > > A system admin of the machine said it is purely vanilla > > installation without any security (SE) settings. > > I'm not sysadmin and have little knowledge on Fedora linux > > so I ask you for help .. > > > > Thanks for any friendly suggestion! > > > > GB> > > > > > > > > > From owner-chemistry@ccl.net Sat Dec 17 18:01:01 2005 From: "Maciej Haranczyk maharan^^chem.univ.gda.pl" To: CCL Subject: CCL: atomic radii for shape and EP calculation Message-Id: <-30353-051217164806-4621-VthzCcAUNqu6Iv+2AZKPLQ]=[server.ccl.net> X-Original-From: Maciej Haranczyk Content-Type: TEXT/PLAIN; charset=US-ASCII Date: Sat, 17 Dec 2005 21:36:14 +0100 (CET) MIME-Version: 1.0 Sent to CCL by: Maciej Haranczyk [maharan\a/chem.univ.gda.pl] Dear All, I would like to analyse shape of the molecule and the electrostatic potential on the surface. I wrote a program that calculates points on the molecular surface which is defined similarly to Connolly surface (van der Walls surface of the molecule). I have a problem to decide on the set of atomic radii that I should use to generate the surface. I got confused when I searched the web and I found that sets of radii are quite different between software packages. Could anyone recommend me a set of radii that will work for shape and EP analysis (with a reference)? I study DNA so I need radii of H,O,N,P,C and Na countercations. Thanks, Maciek -- Maciek Haranczyk maharan%a%chem.univ.gda.pl From owner-chemistry@ccl.net Sat Dec 17 18:41:01 2005 From: "Delwar Hossain hossaind2004]|[yahoo.com" To: CCL Subject: CCL:G: How to use PW91 and LYP in G03 Message-Id: <-30354-051217170744-5744-v1U8dJUBFeDs+yV8EKi3+Q**server.ccl.net> X-Original-From: Delwar Hossain Content-Transfer-Encoding: 8bit Content-Type: multipart/alternative; boundary="0-1306005483-1134853658=:72491" Date: Sat, 17 Dec 2005 13:07:38 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: Delwar Hossain [hossaind2004:-:yahoo.com] --0-1306005483-1134853658=:72491 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Dear sir, I am trying to use LYP and PW91 in G03. But I got an error message when I submit the job. I therefore request you to guide me how to use the LYP and Pw91 in G03 program. input file: %chk=/work5/r0822/POSST12D6h/pt10D5h.chk %mem=200MB %nprocl=1 #T PW91/6-311G OPT PT10D5h-311G** 0 1 Si -0.0000003145 -2.7209281997 1.5981088866 Si -2.5873881549 -0.8401230504 1.5987192355 output: ****************************************** Gaussian 03: IA32L-G03RevC.02 12-Jun-2004 17-Dec-2005 ****************************************** %chk=/work5/r0822/POSST12D6h/pt10D5h.chk %mem=200MB %nprocl=1 Will use up to 1 processors via Linda. ------------------ #T PW91/6-311G OPT ------------------ QPERR --- A SYNTAX ERROR WAS DETECTED IN THE INPUT LINE. #T PW91/6-311G OPT ' Last state="GCL" TCursr= 1020 LCursr= 3 Error termination via Lnk1e in /usr/local/apps/g03/l1.exe at Sat Dec 17 14:51:07 2005. Job cpu time: 0 days 0 hours 0 minutes 0.1 seconds. File lengths (MBytes): RWF= 7 Int= 0 D2E= 0 Chk= 37 Scr= 1 __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com --0-1306005483-1134853658=:72491 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: 8bit

Dear sir,

I am trying to use LYP and PW91 in G03. But I got an error message when I submit the job.

I therefore request you to guide me how to use the LYP and Pw91 in G03 program.

input file:

%chk=/work5/r0822/POSST12D6h/pt10D5h.chk
%mem=200MB
%nprocl=1
#T PW91/6-311G OPT

PT10D5h-311G**

0 1
Si -0.0000003145 -2.7209281997 1.5981088866
Si -2.5873881549 -0.8401230504 1.5987192355

output:

******************************************
Gaussian 03: IA32L-G03RevC.02 12-Jun-2004
                17-Dec-2005
******************************************
%chk=/work5/r0822/POSST12D6h/pt10D5h.chk
%mem=200MB
%nprocl=1
Will use up to    1 processors via Linda.
------------------
#T PW91/6-311G OPT
------------------
QPERR --- A SYNTAX ERROR WAS DETECTED IN THE INPUT LINE.
#T PW91/6-311G OPT
    '
Last state="GCL"
TCursr= 1020 LCursr=    3
Error termination via Lnk1e in /usr/local/apps/g03/l1.exe at Sat Dec 17 14:51:07 2005.
Job cpu time: 0 days 0 hours 0 minutes 0.1 seconds.
File lengths (MBytes): RWF=      7 Int=      0 D2E=      0 Chk=     37 Scr=      1

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http://mail.yahoo.com --0-1306005483-1134853658=:72491-- From owner-chemistry@ccl.net Sat Dec 17 21:17:00 2005 From: "Martijn Zwijnenburg martijn*|*ri.ac.uk" To: CCL Subject: CCL:G: How to use PW91 and LYP in G03 Message-Id: <-30355-051217203253-28714-vbSareQRVtiW0lqYll/27A-$-server.ccl.net> X-Original-From: "Martijn Zwijnenburg" Content-Type: multipart/alternative; boundary="----=_NextPart_000_0970_01C6036B.B99EBD90" Date: Sun, 18 Dec 2005 00:41:03 -0000 MIME-Version: 1.0 Sent to CCL by: "Martijn Zwijnenburg" [martijn|,|ri.ac.uk] This is a multi-part message in MIME format. ------=_NextPart_000_0970_01C6036B.B99EBD90 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hi Delwar, LYP and PW91 are only the correlation part (in the case of LYP) or = either the correlation or exchange part (in the case of PW91) of the = exchange-correlation functional. LYP needs to be combined with a = exchange functional (e.g. the Becke88 exchange, leading to BLYP), while = the correlation functional PW91 can either be combined with the PW91 = exchange functional of the same authors (leading to PW91PW91) or any = other exchange functional (e.g. Becke 88 exchange leading to BPW91).=20 For more details check the online manual: = http://www.gaussian.com/g_ur/k_dft.htm Cheers Martijn ----- Original Message -----=20 > From: "Delwar Hossain hossaind2004]|[yahoo.com" = To: "Zwijnenburg, Martin " Sent: Saturday, December 17, 2005 11:58 PM Subject: CCL:G: How to use PW91 and LYP in G03 > Sent to CCL by: Delwar Hossain [hossaind2004:-:yahoo.com] > --0-1306005483-1134853658=3D:72491 > Content-Type: text/plain; charset=3Diso-8859-1 > Content-Transfer-Encoding: 8bit >=20 > Dear sir, > I am trying to use LYP and PW91 in G03. But I got an error message = when I submit the job.=20 > I therefore request you to guide me how to use the LYP and Pw91 in = G03 program. > =20 > input file: > =20 > %chk=3D/work5/r0822/POSST12D6h/pt10D5h.chk > %mem=3D200MB > %nprocl=3D1 > #T PW91/6-311G OPT > =20 > PT10D5h-311G** > =20 > 0 1 > Si -0.0000003145 -2.7209281997 1.5981088866 > Si -2.5873881549 -0.8401230504 1.5987192355 > =20 > =20 > =20 > output: > =20 > ****************************************** > Gaussian 03: IA32L-G03RevC.02 12-Jun-2004 > 17-Dec-2005 > ****************************************** > %chk=3D/work5/r0822/POSST12D6h/pt10D5h.chk > %mem=3D200MB > %nprocl=3D1 > Will use up to 1 processors via Linda. > ------------------ > #T PW91/6-311G OPT > ------------------ > QPERR --- A SYNTAX ERROR WAS DETECTED IN THE INPUT LINE. > #T PW91/6-311G OPT > ' > Last state=3D"GCL" > TCursr=3D 1020 LCursr=3D 3 > Error termination via Lnk1e in /usr/local/apps/g03/l1.exe at Sat Dec = 17 14:51:07 2005. > Job cpu time: 0 days 0 hours 0 minutes 0.1 seconds. > File lengths (MBytes): RWF=3D 7 Int=3D 0 D2E=3D 0 = Chk=3D 37 Scr=3D 1 >=20 >=20 > __________________________________________________ > Do You Yahoo!? > Tired of spam? Yahoo! Mail has the best spam protection around=20 > http://mail.yahoo.com=20 > --0-1306005483-1134853658=3D:72491 > Content-Type: text/html; charset=3Diso-8859-1 > Content-Transfer-Encoding: 8bit >=20 >

Dear sir,

I am trying to use LYP and = PW91 in G03. But I got an error message when I submit the job.

I therefore request you to guide me how to use the LYP and Pw91 in = G03 program.

input file:

%chk=3D/work5/r0822/POSST12D6h/pt10D5h.chk
%mem=3D200MB=
%nprocl=3D1
#T PW91/6-311G OPT

PT10D5h-311G**

0 = 1
Si -0.0000003145 -2.7209281997 = 1.5981088866
Si -2.5873881549 = -0.8401230504 1.5987192355

output:

******************************************
Gaussian = 03: IA32L-G03RevC.02 = 12-Jun-2004
         &nbs= p;      > = 17-Dec-2005
******************************************
= %chk=3D/work5/r0822/POSST12D6h/pt10D5h.chk
%mem=3D200MB
= ;%nprocl=3D1
Will use up to    1 processors via = Linda.
------------------
#T PW91/6-311G = OPT
------------------
QPERR --- A SYNTAX ERROR WAS = DETECTED IN THE INPUT LINE.
#T PW91/6-311G = OPT
    '
Last = state=3D"GCL"
TCursr=3D 1020 LCursr=3D    = 3
Error termination via Lnk1e in /usr/local/apps/g03/l1.exe at = Sat Dec 17 14:51:07 2005.
Job cpu time: 0 days 0 = hours 0 minutes 0.1 seconds.
File lengths = (MBytes): RWF=3D      7 = Int=3D      0 = D2E=3D      0 Chk=3D     37 = Scr=3D      = 1

__________________________________________________
Do = You Yahoo!?
Tired o! > f spam?=20 > Yahoo! Mail has the best spam protection around =
http://mail.yahoo.com=20 > --0-1306005483-1134853658=3D:72491-- >=20 >=20 >=20 > -=3D This is automatically added to each message by the mailing script = =3D- > To recover the email address of the author of the message, please = change>=20>=20>=20 > Subscribe/Unsubscribe:=20>=20>=20 > Job advertisements: http://www.ccl.net/jobs=20 >=20 > Search Messages: http://www.ccl.net/htdig (login: ccl, Password: = search) >=20>=20>=20 > =>=20 >=20 > ------=_NextPart_000_0970_01C6036B.B99EBD90 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable

Hi Delwar,

LYP and PW91 are only = the correlation=20 part (in the case of LYP) or either the correlation or exchange part (in = the=20 case of PW91) of the exchange-correlation functional. LYP needs to be = combined=20 with a exchange functional (e.g. the Becke88 exchange, leading to = BLYP),=20 while the correlation functional PW91 can either be combined with the = PW91=20 exchange functional of the same authors (leading to PW91PW91) or any = other=20 exchange functional (e.g. Becke 88 exchange leading to=20 BPW91).

For more details check the online = manual: http://www.gaussian.com/g= _ur/k_dft.htm

Cheers

Martijn

----- Original Message -----

From: "Delwar Hossain = hossaind2004]|[yahoo.com"=20 <owner-chemistry(a)ccl.net>

To: "Zwijnenburg, Martin " = <m.a.zwijnenburg(a)tnw.tudelft.nl>

Sent: Saturday, December 17, 2005 11:58 = PM

Subject: CCL:G: How to use PW91 and LYP = in=20 G03

> Sent to CCL by: Delwar Hossain = [hossaind2004:-:yahoo.com]
>=20 --0-1306005483-1134853658=3D:72491
> Content-Type: text/plain;=20 charset=3Diso-8859-1
> Content-Transfer-Encoding: 8bit
> =
> Dear=20 sir,
> I am trying to use LYP and PW91 in G03. But I got an = error=20 message when I submit the job.
> I therefore request you to = guide=20 me how to use the LYP and Pw91 in G03 program.
>  =20
> input file:
>
>=20 %chk=3D/work5/r0822/POSST12D6h/pt10D5h.chk
> %mem=3D200MB
>=20 %nprocl=3D1
> #T PW91/6-311G OPT
>   =
> =20 PT10D5h-311G**
>
> 0=20 1
> Si    -0.0000003145 = -2.7209281997 =20 1.5981088866
> Si    -2.5873881549 =20 -0.8401230504 1.5987192355
>   =
>  =20
>
> output:
>  =20
>  =20 ******************************************
> Gaussian = 03: =20 IA32L-G03RevC.02=20 12-Jun-2004
>         =       =20 17-Dec-2005
> ******************************************
&g= t; %chk=3D/work5/r0822/POSST12D6h/pt10D5h.chk
> %mem=3D20= 0MB
> %nprocl=3D1
> Will=20 use up to    1 processors via=20 Linda.
> ------------------
> #T PW91/6-311G=20 OPT
> ------------------
> QPERR --- A SYNTAX = ERROR WAS=20 DETECTED IN THE INPUT LINE.
> #T PW91/6-311G=20 OPT
>    '
> Last=20 state=3D"GCL"
> TCursr=3D 1020 LCursr=3D   =20 3
> Error termination via Lnk1e in /usr/local/apps/g03/l1.exe = at Sat=20 Dec 17 14:51:07 2005.
> Job cpu time: 0 days 0=20 hours 0 minutes 0.1 seconds.
> File lengths=20 (MBytes): RWF=3D      7=20 Int=3D      0 = D2E=3D      0=20 Chk=3D     37 Scr=3D      = 1
>=20
>
> = __________________________________________________
> Do=20 You Yahoo!?
> Tired of spam? Yahoo! Mail has the best spam=20 protection around
> http://mail.yahoo.com=20
> --0-1306005483-1134853658=3D:72491
> Content-Type: = text/html;=20 charset=3Diso-8859-1
> Content-Transfer-Encoding: 8bit
> =
>=20 <DIV id=3DRTEContent>Dear sir,</DIV> <DIV>I am = trying to=20 use LYP and PW91 in G03. But I got an error message when I submit the = job.=20 </DIV> <DIV>I therefore request you to guide me how to = use the=20 LYP and Pw91 in G03 program.</DIV> =20 <DIV> </DIV> <DIV>input = file:</DIV> =20 <DIV> <BR>%chk=3D/work5/r0822/POSST12D6h/pt10D5h.chk= <BR>%mem=3D200MB<BR>%nprocl=3D1<BR>#T=20 PW91/6-311G  OPT</DIV> =20 <DIV> </DIV> =20 <DIV>PT10D5h-311G**</DIV> =20 <DIV> </DIV> <DIV>0=20 1<BR> Si    = -0.0000003145 =20 -2.7209281997 =20 1.5981088866<BR> Si   =20 -2.5873881549  -0.8401230504  = 1.5987192355</DIV> =20 <DIV> </DIV> = <DIV> </DIV> =20 <DIV> </DIV> = <DIV>output:</DIV> =20 <DIV> </DIV> =20 <DIV> ******************************************<BR>=  Gaussian=20 03:  IA32L-G03RevC.02=20 12-Jun-2004<BR>     &a= mp;nbsp;      &= nbsp;  
> 17-Dec-2005<BR> ***= ***************************************<BR> %chk=3D/work5/= r0822/POSST12D6h/pt10D5h.chk<BR> %mem=3D200MB<BR>&am= p;nbsp;%nprocl=3D1<BR> Will=20 use up to    1 processors via=20 Linda.<BR> ------------------<BR> #T = PW91/6-311G=20 OPT<BR> ------------------<BR>  QPERR --- = A SYNTAX=20 ERROR WAS DETECTED IN THE INPUT LINE.<BR> #T PW91/6-311G=20 OPT<BR>    '<BR> Last=20 state=3D"GCL"<BR> TCursr=3D 1020=20 LCursr=3D    3<BR> Error = termination via=20 Lnk1e in /usr/local/apps/g03/l1.exe at Sat Dec 17 14:51:07=20 2005.<BR> Job cpu time:  0 days  0=20 hours  0 minutes  0.1 seconds.<BR> File = lengths=20 (MBytes):  = RWF=3D      7=20 Int=3D      0=20 D2E=3D      0=20 Chk=3D     37=20 Scr=3D     =20 1<BR></DIV><p>_________________________________________= _________<br>Do=20 You Yahoo!?<br>Tired o!
> f spam?
> Yahoo! = Mail has=20 the best spam protection around <br>http://mail.yahoo.com
> = --0-1306005483-1134853658=3D:72491--
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> = To recover=20 the email address of the author of the message, please change
> = the=20 strange characters on the top line to the (a) sign. You can also
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>
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>=20<= BR>>=20
>
> ------=_NextPart_000_0970_01C6036B.B99EBD90-- From owner-chemistry@ccl.net Sat Dec 17 21:52:02 2005 From: "D. Boyd boyd||chem.iupui.edu" To: CCL Subject: CCL: Is there any book/review/web to learn QSAR/QSAR-3D from the basis? Message-Id: <-30356-051217173224-6672-ein0qKRl9bt+84V4SySLVw.:.server.ccl.net> X-Original-From: "D. Boyd" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; format=flowed Date: Sat, 17 Dec 2005 17:32:17 -0500 Mime-Version: 1.0 (Apple Message framework v623) Sent to CCL by: "D. Boyd" [boyd(a)chem.iupui.edu] Gerard, I was out of town and just now saw your query. For reviews, I recommend the following. The first one mentions pesticides in the title, but is a general introduction to QSAR. E. L. Plummer, in Reviews in Computational Chemistry, K. B. Lipkowitz and D. B. Boyd, Eds., VCH Publishers, New York, 1990, Vol. 1, pp. 119-168. The Application of Quantitative Design Strategies in Pesticide Design. T. I. Oprea and C. L. Waller, in Reviews in Computational Chemistry, K. B. Lipkowitz and D. B. Boyd, Eds., Wiley-VCH, New York, 1997, Vol. 11, pp. 127-182. Theoretical and Practical Aspects of Three-Dimensional Quantitative Structure-Activity Relationships. G. Greco, E. Novellino, and Y. C. Martin, in Reviews in Computational Chemistry, K. B. Lipkowitz and D. B. Boyd, Eds., Wiley-VCH, New York, 1997, Vol. 11, pp. 183-240. Approaches to Three-Dimensional Quantitative Structure-Activity Relationships. Don From owner-chemistry@ccl.net Sat Dec 17 22:27:01 2005 From: "Jamal Uddin uddin-#-rice.edu" To: CCL Subject: CCL:G: How to use PW91 and LYP in G03 Message-Id: <-30357-051217204629-29664-xFImrP3qlIIb3DutcwnSfA{}server.ccl.net> X-Original-From: "Jamal Uddin" Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Sat, 17 Dec 2005 18:56:13 -0600 MIME-Version: 1.0 Sent to CCL by: "Jamal Uddin" [uddin(-)rice.edu] Use BPW91 and BLYP to describe DFT in the route card (e. g. #T BPW91/6-311G). Here, B stands for the Becke *Exchange* functional and PW91 (or LYP) stands for the Perdew/Wang 91 *Correlation* functional. Hope this helps. Jamal -----Original Message----- > From: owner-chemistry]![ccl.net [mailto:owner-chemistry]![ccl.net] Sent: Saturday, December 17, 2005 5:55 PM To: UDDIN, JAMAL Subject: CCL:G: How to use PW91 and LYP in G03 Sent to CCL by: Delwar Hossain [hossaind2004:-:yahoo.com] --0-1306005483-1134853658=:72491 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Dear sir, I am trying to use LYP and PW91 in G03. But I got an error message when I submit the job. I therefore request you to guide me how to use the LYP and Pw91 in G03 program. input file: %chk=/work5/r0822/POSST12D6h/pt10D5h.chk %mem=200MB %nprocl=1 #T PW91/6-311G OPT PT10D5h-311G** 0 1 Si -0.0000003145 -2.7209281997 1.5981088866 Si -2.5873881549 -0.8401230504 1.5987192355 output: ****************************************** Gaussian 03: IA32L-G03RevC.02 12-Jun-2004 17-Dec-2005 ****************************************** %chk=/work5/r0822/POSST12D6h/pt10D5h.chk %mem=200MB %nprocl=1 Will use up to 1 processors via Linda. ------------------ #T PW91/6-311G OPT ------------------ QPERR --- A SYNTAX ERROR WAS DETECTED IN THE INPUT LINE. #T PW91/6-311G OPT ' Last state="GCL" TCursr= 1020 LCursr= 3 Error termination via Lnk1e in /usr/local/apps/g03/l1.exe at Sat Dec 17 14:51:07 2005. Job cpu time: 0 days 0 hours 0 minutes 0.1 seconds. File lengths (MBytes): RWF= 7 Int= 0 D2E= 0 Chk= 37 Scr= 1 __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com --0-1306005483-1134853658=:72491 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: 8bit

Dear sir,

I am trying to use LYP and PW91 in G03. But I got an error message when I submit the job.

I therefore request you to guide me how to use the LYP and Pw91 in G03 program.

input file:

%chk=/work5/r0822/POSST12D6h/pt10D5h.chk
%mem=200MB
%np rocl=1
#T PW91/6-311G OPT

PT10D5h-311G**

0 1
Si -0.0000003145 -2.7209281997 1.5981088866
Si -2.5873881549 -0.8401230504 1.5987192355

output:

******************************************
Gaussian 03: IA32L-G03RevC.02 12-Jun-2004
          & nbsp;     17-Dec-2005
******************************************
%ch k=/work5/r0822/POSST12D6h/pt10D5h.chk
%mem=200MB
%nprocl=1
Will use up to    1 processors via Linda.
------------------
#T PW91/6-311G OPT
------------------
QPERR --- A SYNTAX ERROR WAS DETECTED IN THE INPUT LINE.
#T PW91/6-311G OPT
    '
Last state="GCL"
TCursr= 1020 LCursr=    3
Error termination via Lnk1e in /usr/local/apps/g03/l1.exe at Sat Dec 17 14:51:07 2005.
Job cpu time: 0 days 0 hours 0 minutes 0.1 seconds.
File lengths (MBytes): RWF=      7 Int=      0 D2E=      0 Chk=     37 Scr=      1

__________________________________________________
Do You Yahoo!?
Tired o! f spam? Yahoo! Mail has the best spam protection around
http://mail.yahoo.com --0-1306005483-1134853658=:72491--http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Sat Dec 17 23:02:00 2005 From: "Yun Wang wangyun22%%yahoo.com" To: CCL Subject: CCL:G: adsorption, ab initio study Message-Id: <-30358-051217204949-30314-ETImp6Ur5gQD+z2RUdVkjA!^!server.ccl.net> X-Original-From: Yun Wang Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-1 Date: Sat, 17 Dec 2005 16:49:43 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: Yun Wang [wangyun22|yahoo.com] It depents on your systems. If you study the adsorption on solid surface with periodic symmetry, slab model is better. There are several free software: CPMD, PWscf,FHI98md etc. If you want to employ cluter model, you can do calculation with Gaussian, Gamess etc. Both of them need many computation time. The computer should be very good. Best wishes. Yun Wang --- "Jinsong Zhao jszhao!^!mail.hzau.edu.cn" wrote: > Sent to CCL by: "Jinsong Zhao" > [jszhao[a]mail.hzau.edu.cn] > Dear all, > > I think someone here do researches on adsorption > using ab initio method. > > I hope you would like to point me out how to > construct a model that will > be suite for computation using ab initio methods. > > I just know there are two models widely used in > adsorption study, one is > cluster model, the other is SLAB model. However, I > don't know how to > construct such model. And what's the suitable > program? > > Any comments, suggestions or tutorials will be > really appreciated! > > Thanks in advance! > > Jinsong Zhao > College of Resources and Environment > Huazhong Agricultural University > Wuhan 430070, P.R. China > E-mail: jszhao[]mail.hzau.edu.cn > > > > -= This is automatically added to each message by > the mailing script =- > To recover the email address of the author of the > message, please change > the strange characters on the top line to the .. > sign. You can also > look up the X-Original-From: line in the mail > header.> > E-mail to administrators: CHEMISTRY-REQUEST .. ccl.net > or use> > Before posting, check wait time at: > http://www.ccl.net> > Search Messages: http://www.ccl.net/htdig (login: > ccl, Password: search) > > If your mail bounces from CCL with 5.7.1 error, > check:> > RTFI: > http://www.ccl.net/chemistry/aboutccl/instructions/> > > > __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com