From owner-chemistry@ccl.net Wed May 23 08:55:00 2007 From: "elisabetta a. venuti venuti||ms.fci.unibo.it" To: CCL Subject: CCL:G: termination via Lnk1e in /cineca/prod/gaussian/03d02-xlf10 Message-Id: <-34327-070523072138-21187-6c1KA3L49leBsmVvrM5Pzg{=}server.ccl.net> X-Original-From: "elisabetta a. venuti" Date: Wed, 23 May 2007 07:21:34 -0400 Sent to CCL by: "elisabetta a. venuti" [venuti[*]ms.fci.unibo.it] Dear All I have submitted in Gaussian the following command file: ----------------------------------------- %mem=300MW %CHK=h2pc-D2h-sym1.chk P B3LYP/6-31G(d) opt=(tight) freq=(hpmodes,raman) POP=(full,ESPdipole ) h2pc-D2h-sym1.com - gaussian input, phthcyanine+OCH3, perturbed symmetry 0 1 C -0.000000 2.762282 1.096975 C -0.000000 2.762282 -1.096975 C 0.000000 -2.762282 1.096975 C 0.000000 -2.762282 -1.096975 C -0.000000 1.146013 2.790695 C 0.000000 1.146013 -2.790695 C -0.000000 -1.146013 2.790695 C 0.000000 -1.146013 -2.790695 C -0.000000 0.706787 4.175420 C 0.000000 0.706787 -4.175420 C -0.000000 -0.706787 4.175420 C 0.000000 -0.706787 -4.175420 C -0.000000 4.174996 0.702182 C -0.000000 4.174996 -0.702182 C 0.000000 -4.174996 0.702182 C 0.000000 -4.174996 -0.702182 C -0.000000 1.426312 5.373363 C 0.000000 1.426312 -5.373363 C -0.000000 -1.426312 5.373363 C 0.000000 -1.426312 -5.373363 C -0.000000 5.365439 1.424935 C -0.000000 5.365439 -1.424935 C 0.000000 -5.365439 1.424935 C 0.000000 -5.365439 -1.424935 C -0.000000 0.705149 6.563367 C 0.000000 0.705149 -6.563367 C -0.000000 -0.705149 6.563367 C 0.000000 -0.705149 -6.563367 C -0.000000 6.561439 0.702734 C -0.000000 6.561439 -0.702734 C 0.000000 -6.561439 0.702734 C 0.000000 -6.561439 -0.702734 C -0.000000 0.667004 9.014488 C 0.000000 -9.014883 0.667205 C 0.000000 -0.667004 -9.014488 C -0.000000 9.014883 -0.667205 H -0.000000 2.511561 5.363534 H 0.000000 2.511561 -5.363534 H -0.000000 -2.511561 5.363534 H 0.000000 -2.511561 -5.363534 H 0.000000 1.234998 -7.511862 H -0.000000 -1.234998 7.511862 H -0.000000 7.509334 1.234173 H 0.000000 -7.509334 -1.234173 H -0.000000 -0.000000 1.011427 H 0.000000 0.000000 -1.011427 H -0.000000 5.357360 2.510542 H -0.000000 5.357360 -2.510542 H 0.000000 -5.357360 2.510542 H 0.000000 -5.357360 -2.510542 H -0.000000 -0.387058 8.717875 H -0.913809 0.966544 9.538181 H 0.913809 0.966544 9.538181 H 0.000000 -8.718836 -0.387016 H -0.913809 -9.538416 0.967026 H 0.913809 -9.538416 0.967026 H 0.000000 0.387058 -8.717875 H -0.913809 -0.966544 -9.538181 H 0.913809 -0.966544 -9.538181 H -0.000000 8.718836 0.387016 H -0.913809 9.538416 -0.967026 H 0.913809 9.538416 -0.967026 N 0.000000 -2.398972 2.382722 N 0.000000 -2.398972 -2.382722 N -0.000000 1.949803 0.000000 N 0.000000 -1.949803 0.000000 N -0.000000 -0.000000 2.025410 N 0.000000 0.000000 -2.025410 N -0.000000 2.398972 2.382722 N -0.000000 2.398972 -2.382722 O 0.000000 -7.800084 1.402503 O 0.000000 -1.402954 -7.800084 O -0.000000 1.402954 7.800084 O -0.000000 7.800084 -1.402503 ------------------------------------------------------------------------------------------------- After about 43 m cpu time I get (more than once) the following exit in the .log file Leave Link 601 at Tue May 22 23:23:36 2007, MaxMem= 314572800 cpu: 15.2 (Enter /cineca/prod/gaussian/03d02-xlf10/g03/l602.exe) Merz-Kollman atomic radii used. No vectors left in VDWSrf. Error termination via Lnk1e in /cineca/prod/gaussian/03d02-xlf10/g03/l602.exe at Tue May 22 23:23:37 2007. Job cpu time: 0 days 0 hours 43 minutes 7.2 seconds. File lengths (MBytes): RWF= 381 Int= 0 D2E= 0 Chk= 16 Scr= 2 ============================================== Any clues? I really can't understand what's wrong ....... thanks for help Elisabetta Venuti venuti-$-ms.fci.unibo.it From owner-chemistry@ccl.net Wed May 23 09:30:00 2007 From: "Martin Fan fanfengeta||163.com" To: CCL Subject: CCL:G: Problems about Test528 in Gaussian 03 Message-Id: <-34328-070523022037-25401-tj+775NnS7/RvPy7U9iqNg|,|server.ccl.net> X-Original-From: "Martin Fan" Date: Wed, 23 May 2007 02:20:34 -0400 Sent to CCL by: "Martin Fan" [fanfengeta-.-163.com] Dear all, The QM/MM test which named TEST528 in Gaussian03 had been studied. Some problems puzzled me and ask for help here. Some of the input file is shown below: %mem=16mw p ONIOM(RHF/6-31G(d):AM1 sparse:AMBER=softfirst) pop=none test scf=xqc Gaussian Test Job 528: HIV-1 integrase catalytic core, oniom opt -1 1 -1 1 -1 1 1 1 C-C-0.799386 30.93051 32.93674 17.38851 H O-O2--0.801386 31.56959 34.00780 17.52633 H O-O2--0.801386 30.81174 32.39480 16.26804 H C-C-0.799386 34.71479 32.32202 17.14600 H O-O2--0.801386 35.58428 31.74845 16.45848 H O-O2--0.801386 34.15963 33.40921 16.85468 H C-C-0.805386 27.54270 29.54653 13.41746 H O-O2--0.818786 27.70889 30.30501 14.39981 H O-O2--0.818786 26.64518 29.72404 12.56257 H O-O2-1.99997 32.98852 34.92098 16.53451 H ..... HrmStr1 C H4 367.0 1.080 HrmStr1 C H5 367.0 1.080 HrmBnd1 CT C H4 35.0 120.00 HrmBnd1 O C H4 35.0 120.00 HrmBnd1 O2 C H5 35.0 120.00 1. How to difine charges of each part like "-1 1 -1 1 ...",even that the sum of each atomic charge was not equal to -1. 2. When should we define the "HrmStr1, HrmBnd1" showed above where at the end of the input file? 3. How to obtain the part charges of each atom? Thanks very much for any help! From owner-chemistry@ccl.net Wed May 23 10:05:00 2007 From: "elisabetta a. venuti venuti .. ms.fci.unibo.it" To: CCL Subject: CCL:G: gaussian and polarizabilities Message-Id: <-34329-070523054137-10222-iaXKucAK0t9kmO3ETlg+sQ(-)server.ccl.net> X-Original-From: "elisabetta a. venuti" Date: Wed, 23 May 2007 05:41:33 -0400 Sent to CCL by: "elisabetta a. venuti" [venuti^_^ms.fci.unibo.it] 23/4/2007 15:25 Dear All Some time ago I wrote Guassian Inc. support asking whether it was possible to have the cartesian components of the transition dipole moments (derivatives of the dipole vectors with respect to the normal coordinates) printed out, together with the corresponding tensor derivatives for the polarizabilities. The answer was to use an additional print in overlay 7, namely the IOP IOP(7/33=1) So I ran my program with the following instructions in the .com file ------------------------------------------------------------------- P B3LYP/6-31G(d) opt=(tight,calcall) freq=(hpmodes,raman) Polar Symm=Loose IOP(7/33=1) -------------------------------------------------------------------- followed by (since for some technical reason the job was not completed) CHK=ru-C2h.chk P B3LYP/6-31G(d) opt=(tight,calcall) freq=(hpmodes,raman) Polar=restart Symm=Loose IOP(7/33=1) ---------------------------------------------------------------------- Now I do have some trouble to understand the output, and the Gaussian support is not answering! No problem for the dipole derivatives, expressed, for instance, as "Dipole derivatives wrt mode 118: 1.77524D-07 -4.58393D-07 -8.57884D-07" since there are three components, as I expect them to be. I'd say no problem with the static polarizability, either, if it is given by : " Polarizability= 4.97409853D+02 3.03356725D+01 2.99469021D+02 2.04374917D-06-2.82284822D-06 6.11420666D+02" However I can't find the way of interpreting the output lines (one for each vib. mode) "Vibrational polarizability contributions from mode 119 0.0000000 0.0000000 0.1189699" Is here the derivative of the polarizability tensor wrt the mode? It does not look like, as I expect six components. So what is this? and how can i get the actual derivatives? Thanks for any answer Elisabetta Venuti venuti-*-ms.fci.unibo.it From owner-chemistry@ccl.net Wed May 23 10:40:00 2007 From: "Martin Fan fanfengeta{:}163.com" To: CCL Subject: CCL:G: Problems about Test528 in Gaussian 03 Message-Id: <-34330-070523020658-24888-D339fVZUgIHm149P7W9dbA^^server.ccl.net> X-Original-From: "Martin Fan" Date: Wed, 23 May 2007 02:06:54 -0400 Sent to CCL by: "Martin Fan" [fanfengeta|163.com] Dear all, The QM/MM test which named TEST528 in Gaussian03 had been studied. Some problems puzzled me and ask for help here. Some of the input file is shown below: %mem=16mw p ONIOM(RHF/6-31G(d):AM1 sparse:AMBER=softfirst) pop=none test scf=xqc Gaussian Test Job 528: HIV-1 integrase catalytic core, oniom opt -1 1 -1 1 -1 1 1 1 C-C-0.799386 30.93051 32.93674 17.38851 H O-O2--0.801386 31.56959 34.00780 17.52633 H O-O2--0.801386 30.81174 32.39480 16.26804 H C-C-0.799386 34.71479 32.32202 17.14600 H O-O2--0.801386 35.58428 31.74845 16.45848 H O-O2--0.801386 34.15963 33.40921 16.85468 H C-C-0.805386 27.54270 29.54653 13.41746 H O-O2--0.818786 27.70889 30.30501 14.39981 H O-O2--0.818786 26.64518 29.72404 12.56257 H O-O2-1.99997 32.98852 34.92098 16.53451 H ..... HrmStr1 C H4 367.0 1.080 HrmStr1 C H5 367.0 1.080 HrmBnd1 CT C H4 35.0 120.00 HrmBnd1 O C H4 35.0 120.00 HrmBnd1 O2 C H5 35.0 120.00 1. How to difine charges of each part like "-1 1 -1 1 ...",even that the sum of each atomic charge was not equal to -1. 2. When should we define the "HrmStr1, HrmBnd1" showed above where at the end of the input file? 3. How to obtain the part charges of each atom? Thanks very much for any help! From owner-chemistry@ccl.net Wed May 23 11:29:01 2007 From: "Yubo Fan yubofan,mail.chem.tamu.edu" To: CCL Subject: CCL: Amber 9 on AIX 5.3 Message-Id: <-34331-070523110655-22867-2MQoujLY+47KVWgYVJ67Yg() server.ccl.net> X-Original-From: "Yubo Fan" Content-Type: multipart/alternative; boundary="----=_NextPart_000_001B_01C79D22.48C64230" Date: Wed, 23 May 2007 10:08:17 -0500 MIME-Version: 1.0 Sent to CCL by: "Yubo Fan" [yubofan%%mail.chem.tamu.edu] This is a multi-part message in MIME format. ------=_NextPart_000_001B_01C79D22.48C64230 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hello, everyone, I compiled Amber 9 on a IBM p5-575 cluster with AIX 5.3 installed. The = compilation was passed although the NetCDF trajectory format had to be = shut off. Unfortunately, most of my jobs could not run using pmemd on = the IBM machine. In the Amber output file, only the list of the input = files appeared. There is not any error message. But sander can run = correctly with the same input files. Any advice for the compiling of = pmemd on AIX 5.3? Thanks,=20 Yubo =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D Dr. Yubo Fan Email: yubofan^^mail.chem.tamu.edu Department of Chemistry Tel: 1-979-845-5237 Texas A&M University College Station, TX 77843 =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D ------=_NextPart_000_001B_01C79D22.48C64230 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Hello, everyone,
 
I compiled Amber 9 on a IBM p5-575 = cluster with AIX=20 5.3 installed. The compilation was passed although the NetCDF trajectory = format=20 had to be shut off. Unfortunately, most of my jobs could not run using = pmemd on=20 the IBM machine. In the Amber output file, only the list of the input = files=20 appeared. There is not any error message. But sander can run correctly = with the=20 same input files. Any advice for the compiling of pmemd on AIX = 5.3?
 
Thanks,
 
Yubo
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
Dr. Yubo=20 Fan           &nbs= p;  =20 Email: yubofan^^mail.chem.tamu.edu=
Department=20 of Chemistry    Tel:   1-979-845-5237
Texas = A&M=20 University
College Station, TX=20 77843
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
------=_NextPart_000_001B_01C79D22.48C64230-- From owner-chemistry@ccl.net Wed May 23 12:04:00 2007 From: "Jeff Hammond jeff.science]![gmail.com" To: CCL Subject: CCL:G: Gaussian Problems Message-Id: <-34332-070523112843-3183-VbpTwCKsLUDflnEjpc8CtA : server.ccl.net> X-Original-From: Jeff Hammond Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 23 May 2007 10:28:13 -0500 MIME-Version: 1.0 Sent to CCL by: Jeff Hammond [jeff.science!=!gmail.com] Recently, it seems that nearly half the messages on this listserve are for Gaussian technical support. To this, I have a few comments: 1. If Gaussian isn't working for you, that's either your fault or Gaussian's. That means either you RTFM or email help|,|gaussian.com. Stop dumping your technical support problems on a list meant to serve the whole computational chemistry community, not just those who are foolish enough to pay for second-rate code. 2. Gaussian should have their own user listserve. They don't, probably because of the cost of hardware and maintenance. Funny how all the free codes can afford this but Gau$$ian cannot. Why don't you tell them to set one up next time you renew your draconian license. 3. Consider saving yourself time and money by going online, downloading a free code which does what you want and comes with great tech support and a user listserve. To preempt the most common objection to using codes other than Gaussian: if you cannot figure out how to make an input file in a format other than Gaussian's, you are too stupid to be a computational chemist. By not using Gaussian, you'll be paying yourself $4,000 to learn a new input format. Here are three codes which can probably replace Gaussian for 99% of its users: Dalton http://www.kjemi.uio.no/software/dalton/dalton.html GAMESS http://www.msg.ameslab.gov/GAMESS/gamess.html NWChem http://www.emsl.pnl.gov/docs/nwchem/nwchem.html Use the scientific brain you claim to have by being on this list and do the math: using Gaussian does not make financial or scientific sense. Jeff From owner-chemistry@ccl.net Wed May 23 13:05:00 2007 From: "=?ISO-8859-1?Q?=D6d=F6n?= Farkas farkas- -chem.elte.hu" To: CCL Subject: CCL: Gaussian Problems Message-Id: <-34333-070523125634-19675-bccXDqANlZfFlZI+RwEa9w~~server.ccl.net> X-Original-From: =?ISO-8859-1?Q?=D6d=F6n?= Farkas Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=UTF-8 Date: Wed, 23 May 2007 18:52:41 +0200 Mime-Version: 1.0 Sent to CCL by: =?ISO-8859-1?Q?=D6d=F6n?= Farkas [farkas---chem.elte.hu] Hi Jeff, Could you just simply not making assumptions on something what you do not use? CCL is a list for everyone in the area and if the messages where "CCL:G:" appears in the subject bother you, just simply use your brain and find the filter in your mail reading application. If it does not have this functionality take your time and find another one. Best wishes, Odon -- Ödön Farkas Associate professor Deparment of Organic Chemistry and Laboratory of Chemical Informatics, Institute of Chemistry, Eötvös Loránd University, Budapest Address: 1/A Pázmány Péter sétány, H-1117 Budapest, Hungary Phone: +36-1-372-2570 Cell phone: +36-30-255-3111 Fax: +36-1-372-2620 URL: http://organ.elte.hu/farkas From owner-chemistry@ccl.net Wed May 23 14:00:00 2007 From: "Nuno A. G. Bandeira nuno.bandeira[*]ist.utl.pt" To: CCL Subject: CCL:G: Gaussian Problems Message-Id: <-34334-070523135208-13003-5zeSk1NdbwDpR5cdakfQfA**server.ccl.net> X-Original-From: "Nuno A. G. Bandeira" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 23 May 2007 18:19:46 +0100 MIME-Version: 1.0 Sent to CCL by: "Nuno A. G. Bandeira" [nuno.bandeira#,#ist.utl.pt] Let's see now. I've used quite a few computational chemistry programs and indeed I agree that you should be flexible enough to use anything. However rather than calling people stupid you should actually compare the programs that you mention with Gaussian. Jeff Hammond jeff.science]![gmail.com wrote: > > To preempt the most common objection to using codes other than Gaussian: > if you cannot figure out how to make an input file in a format other > than Gaussian's, you are too stupid to be a computational chemist. By > not using Gaussian, you'll be paying yourself $4,000 to learn a new > input format. > > Here are three codes which can probably replace Gaussian for 99% of its > users: > > Dalton > http://www.kjemi.uio.no/software/dalton/dalton.html Don't know. Never used it. > GAMESS > http://www.msg.ameslab.gov/GAMESS/gamess.html Painfully slow DFT and hybrids. No analytic second derivatives for unrestricted wavefunctions. No PBC. Strong points are wavefunction based methods. > NWChem > http://www.emsl.pnl.gov/docs/nwchem/nwchem.html No analytic frequencies at all. Draconian distribution policy (they will only send passwords by snail mail). This also means if you're trying to locate a transition state for example these programs will not replace Gaussian 99% of the times. I've never to this day seen a program that can beat Gaussian in speed at computing vibrational frequencies. Not many programs are eclectic as Gaussian nor do they have as big a reputation. It strikes me that some people just hold a grudge against Gaussian Inc. and everyone that uses their products. Not a very scientific attitude in my opinion. Regards, -- Nuno A. G. Bandeira, AMRSC Graduate researcher and molecular sculptor Inorganic and Theoretical Chemistry Group, Faculty of Science University of Lisbon - C8 building, Campo Grande, 1749-016 Lisbon,Portugal http://cqb.fc.ul.pt/intheochem/nuno.html Doctoral student *|* IST,Lisbon -- From owner-chemistry@ccl.net Wed May 23 14:39:00 2007 From: "Joe Leonard jleonard42:_:gmail.com" To: CCL Subject: CCL:G: Gaussian Problems Message-Id: <-34335-070523143628-1068-YdLAKeclsz81pc6UEe4i3A _ server.ccl.net> X-Original-From: Joe Leonard Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Date: Wed, 23 May 2007 13:38:14 -0400 Mime-Version: 1.0 (Apple Message framework v752.2) Sent to CCL by: Joe Leonard [jleonard42]=[gmail.com] Gee, another anti-Gaussian screed... Can we save time by merely referring readers to the CCL archives for the previous discussions/ flame-wars on this topic? These messages have tags in their headers for years - filter the bloody things, or just automatically hit when they come in. From where I sit, there's a whole lot to computational chemistry that doesn't involve QM calculations - much of which, unfortunately, isn't often covered here. Joe Leonard jleonard42**gmail.com (formerly jle**theworld.com) On May 23, 2007, at 11:28 AM, Jeff Hammond jeff.science]![gmail.com wrote: > > Sent to CCL by: Jeff Hammond [jeff.science!=!gmail.com] > Recently, it seems that nearly half the messages on this listserve > are for Gaussian technical support. To this, I have a few comments: > > 1. If Gaussian isn't working for you, that's either your fault or > Gaussian's. That means either you RTFM or email > help.**.gaussian.com. Stop dumping your technical support problems > on a list meant to serve the whole computational chemistry > community, not just those who are foolish enough to pay for second- > rate code. > > 2. Gaussian should have their own user listserve. They don't, > probably because of the cost of hardware and maintenance. Funny > how all the free codes can afford this but Gau$$ian cannot. Why > don't you tell them to set one up next time you renew your > draconian license. > > 3. Consider saving yourself time and money by going online, > downloading a free code which does what you want and comes with > great tech support and a user listserve. > > To preempt the most common objection to using codes other than > Gaussian: if you cannot figure out how to make an input file in a > format other than Gaussian's, you are too stupid to be a > computational chemist. By not using Gaussian, you'll be paying > yourself $4,000 to learn a new input format. > > Here are three codes which can probably replace Gaussian for 99% of > its users: > > Dalton > http://www.kjemi.uio.no/software/dalton/dalton.html > > GAMESS > http://www.msg.ameslab.gov/GAMESS/gamess.html > > NWChem > http://www.emsl.pnl.gov/docs/nwchem/nwchem.html > > Use the scientific brain you claim to have by being on this list > and do the math: using Gaussian does not make financial or > scientific sense. > > Jeff > > > > -= This is automatically added to each message by the mailing > script =- > To recover the email address of the author of the message, please > changehttp://www.ccl.net/chemistry/ > sub_unsub.shtmlConferences: http://server.ccl.net/ > chemistry/announcements/conferences/ > > Search Messages: http://www.ccl.net/htdig (login: ccl, Password: > search)> > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+- > +-+-+ > > > From owner-chemistry@ccl.net Wed May 23 15:14:00 2007 From: "Robert Duke rduke%%email.unc.edu" To: CCL Subject: CCL: Amber 9 on AIX 5.3 Message-Id: <-34336-070523140904-19628-fekAZwaXftnFw1X2fksoHQ*o*server.ccl.net> X-Original-From: "Robert Duke" Content-Type: multipart/alternative; boundary="----=_NextPart_000_004A_01C79D3C.AA9F8C90" Date: Wed, 23 May 2007 13:17:08 -0400 MIME-Version: 1.0 Sent to CCL by: "Robert Duke" [rduke * email.unc.edu] This is a multi-part message in MIME format. ------=_NextPart_000_004A_01C79D3C.AA9F8C90 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Yubo - This is way too little info for me to be able to figure out what is = going on. PMEMD should run fine on ibm sp5 machines, which is what I = presume you are dealing with here. I am not sure about the specific AIX = release, but any issues there should show up in compile/link. Do you = have system folks helping you, or are you trying to do this all on your = own? We run pmemd on at least 5 sp3, sp4, and sp5 machines that I know = of. Regards - Bob Duke ----- Original Message -----=20 From: Yubo Fan yubofan,mail.chem.tamu.edu=20 To: Duke, Robert E =20 Sent: Wednesday, May 23, 2007 11:08 AM Subject: CCL: Amber 9 on AIX 5.3 Hello, everyone, I compiled Amber 9 on a IBM p5-575 cluster with AIX 5.3 installed. The = compilation was passed although the NetCDF trajectory format had to be = shut off. Unfortunately, most of my jobs could not run using pmemd on = the IBM machine. In the Amber output file, only the list of the input = files appeared. There is not any error message. But sander can run = correctly with the same input files. Any advice for the compiling of = pmemd on AIX 5.3? Thanks,=20 Yubo = =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D Dr. Yubo Fan Email: yubofan:_:mail.chem.tamu.edu Department of Chemistry Tel: 1-979-845-5237 Texas A&M University College Station, TX 77843 = =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D ------=_NextPart_000_004A_01C79D3C.AA9F8C90 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Yubo -
This is way too little info for me to be able to = figure out=20 what is going on.  PMEMD should run fine on ibm sp5 machines, which = is what=20 I presume you are dealing with here.  I am not sure about the = specific AIX=20 release, but any issues there should show up in compile/link.  Do = you have=20 system folks helping you, or are you trying to do this all on your = own?  We=20 run pmemd on at least 5 sp3, sp4, and sp5 machines that I know = of.
Regards - Bob Duke
----- Original Message -----
From:=20 Yubo=20 Fan yubofan,mail.chem.tamu.edu
Sent: Wednesday, May 23, 2007 = 11:08=20 AM
Subject: CCL: Amber 9 on AIX = 5.3

Hello, everyone,
 
I compiled Amber 9 on a IBM p5-575 = cluster with=20 AIX 5.3 installed. The compilation was passed although the NetCDF = trajectory=20 format had to be shut off. Unfortunately, most of my jobs could not = run using=20 pmemd on the IBM machine. In the Amber output file, only the list of = the input=20 files appeared. There is not any error message. But sander can run = correctly=20 with the same input files. Any advice for the compiling of pmemd on = AIX=20 5.3?
 
Thanks,
 
Yubo
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
Dr.=20 Yubo=20 = Fan           &nbs= p;  =20 Email: yubofan:_:mail.chem.tamu.edu=
Department=20 of Chemistry    Tel:   = 1-979-845-5237
Texas=20 A&M University
College Station, TX=20 = 77843
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
<= /HTML> ------=_NextPart_000_004A_01C79D3C.AA9F8C90-- From owner-chemistry@ccl.net Wed May 23 15:49:00 2007 From: "Shobe, David David.Shobe]~[sud-chemie.com" To: CCL Subject: CCL:G: GAMESS, Dalton, and NWCHem problems :-) Message-Id: <-34337-070523152020-31025-5GFurxzs5vQRM84ZKtpeZA()server.ccl.net> X-Original-From: "Shobe, David" Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Wed, 23 May 2007 21:19:38 +0200 MIME-Version: 1.0 Sent to CCL by: "Shobe, David" [David.Shobe-x-sud-chemie.com] I downloaded GAMESS last year, but I couldn't even figure out how to run one of the example/test jobs. All I get is a "timed out" message after a few minutes. I guess that makes me even stupider than the people who just don't want to learn a new input format. I was under the impression that there was no tech support for GAMESS. Help.().gaussian.com is sometimes slow, but they usually at least try to help. The other 2 programs you mention won't even run on the second-rate operating system that came with my computer. I won't name the OS, but you can probably guess. And if I changed to Linux, I'd be unable to use most of my non-computational-chemistry software. Jeff is right about one thing though. We certainly could use a Gaussian listserve for Gaussian-specific problems. --David Shobe P.S. I was lucky enough to be a student in 1998, so I never had to pay the full retail price for Gaussian. :-) -----Original Message----- > From: owner-chemistry.().ccl.net [mailto:owner-chemistry.().ccl.net] Sent: Wednesday, May 23, 2007 11:28 AM To: Shobe, David Subject: CCL:G: Gaussian Problems Sent to CCL by: Jeff Hammond [jeff.science!=!gmail.com] Recently, it seems that nearly half the messages on this listserve are for Gaussian technical support. To this, I have a few comments: 1. If Gaussian isn't working for you, that's either your fault or Gaussian's. That means either you RTFM or email help..()..gaussian.com. Stop dumping your technical support problems on a list meant to serve the whole computational chemistry community, not just those who are foolish enough to pay for second-rate code. 2. Gaussian should have their own user listserve. They don't, probably because of the cost of hardware and maintenance. Funny how all the free codes can afford this but Gau$$ian cannot. Why don't you tell them to set one up next time you renew your draconian license. 3. Consider saving yourself time and money by going online, downloading a free code which does what you want and comes with great tech support and a user listserve. To preempt the most common objection to using codes other than Gaussian: if you cannot figure out how to make an input file in a format other than Gaussian's, you are too stupid to be a computational chemist. By not using Gaussian, you'll be paying yourself $4,000 to learn a new input format. Here are three codes which can probably replace Gaussian for 99% of its users: Dalton http://www.kjemi.uio.no/software/dalton/dalton.html GAMESS http://www.msg.ameslab.gov/GAMESS/gamess.html NWChem http://www.emsl.pnl.gov/docs/nwchem/nwchem.html Use the scientific brain you claim to have by being on this list and do the math: using Gaussian does not make financial or scientific sense. Jeffhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txtThis e-mail message may contain confidential and / or privileged information. If you are not an addressee or otherwise authorized to receive this message, you should not use, copy, disclose or take any action based on this e-mail or any information contained in the message. If you have received this material in error, please advise the sender immediately by reply e-mail and delete this message. Thank you. From owner-chemistry@ccl.net Wed May 23 16:30:00 2007 From: "Jeff Hammond jeff.science]-[gmail.com" To: CCL Subject: CCL:G: Corrections w.r.t. NWChem functionality Message-Id: <-34338-070523153858-11136-ycqO2wT5vcc0PZbs5dROOQ _ server.ccl.net> X-Original-From: Jeff Hammond Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 23 May 2007 14:38:17 -0500 MIME-Version: 1.0 Sent to CCL by: Jeff Hammond [jeff.science:_:gmail.com] Your information on NWChem is quite old. I'm running DFT vibrational frequencies right now. > (NWChem) No analytic frequencies at all. Draconian distribution policy (they will > only send passwords by snail mail). Analytic first derivatives are available for every method except those in the TCE and analytic second derivatives for SCF and all common DFT functionals: http://www.emsl.pnl.gov/docs/nwchem/release-notes/dft_functionals.html Fax machines may be draconian to you, but they are secure: http://www.emsl.pnl.gov/docs/nwchem/download.html > This also means if you're trying to locate a transition state for > example these programs will not replace Gaussian 99% of the times. Transition states can be done as well: http://www.emsl.pnl.gov/docs/nwchem/support/faq/optimization.html From owner-chemistry@ccl.net Wed May 23 22:06:01 2007 From: "Caroline M. Taylor cmtaylor---mtu.edu" To: CCL Subject: CCL:G: Gaussian Problems Message-Id: <-34339-070523180449-13466-Lge8lSrXj4NA/Gnw9Ft6Vw+/-server.ccl.net> X-Original-From: "Caroline M. Taylor" Content-Type: TEXT/PLAIN; charset=US-ASCII Date: Wed, 23 May 2007 17:26:47 -0400 (EDT) MIME-Version: 1.0 Sent to CCL by: "Caroline M. Taylor" [cmtaylor- -mtu.edu] Hello, all. In the interests of full disclosure, I have to say that, for electronic structure, my group uses primarily GAMESS, so we may be biased towards packages which are freely available to all, and for which the source is publicly available. I want to quibble with the usage of "draconian" as it's being bandied about in this discussion. Access to NWChem may be a bit tedious, but anyone can get it (independent of other packages they may be using) and requiring a secure distribution of the license passcode is not "excessively harsh and severe," a definition which I do think applies to the Gaussian licensing policies (i.e. if you dare to use something else, we'll take it away from you). It is more than a little bit disingenuous that the package for which one must pay is the one that does not maintain it's own listserve, but rather exploits a personally-hosted and maintained (thank you, Jan, for this wonderful resource!) listserve, rather than suppling it's own. As has been mentioned, computational chemistry on this list used to mean much more than just QM/MM, and I, too, am sorry to see the shift to a more focused environment. CCL is a resource that we're lucky to have, and while there do seem to be more questions to which the answer may justifiably be "RTFM" recently, the community has been commendably patient and continues to be both helpful and interesting. Best, Caroline --------------------------------------------- Caroline M. Taylor, Assistant Professor Department of Chemistry Michigan Technological University 1400 Townsend Dr. Houghton, MI 49931 Ph: 906-487-1645 Fax: 906-487-2061 http://www.chemistry.mtu.edu/pages/faculty/faculty.php?fac=cmtaylor http://www.taylorgroup.chemistry.mtu.edu/ ---------------------------------------------