From owner-chemistry@ccl.net Mon May 29 04:34:00 2006 From: "gas5x.+/-.bancorp.ru" To: CCL Subject: CCL: exam09 and MPI Message-Id: <-31852-060529032506-30038-uOWDocxg9r0n7dZFHIIIsw+/-server.ccl.net> X-Original-From: Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="KOI8-R"; format="flowed" Date: Mon, 29 May 2006 10:24:45 +0400 MIME-Version: 1.0 Sent to CCL by: [gas5x(0)bancorp.ru] Hi Fernando, On Fri, 26 May 2006 09:44:43 -0400 "Fernando Mota Valeri f.mota_-_ub.edu" wrote: > Sent to CCL by: Fernando Mota Valeri [f.mota|ub.edu] > I am trying to run the exam09 ( a MRMP2 in memory >determinant > calculation) job with GAMESS VERSION = 27 JUN 2005 (R2) >in a cluster > with mpi and i obtain the message that follows: > > DIRECT 4-INDEX TRANSFORMATION > SCHWARZ INEQUALITY TEST SKIPPED 0 >INTEGRAL BLOCKS > DDI Process 0: Invalid row dimensions during DDI_Get => >ilo=0 ihi=-1. > A fatal error occurred on DDI Process 0. > DDI Process 0: Killing remaining DDI processes. > DDI Process 1: Invalid row dimensions during DDI_Get => >ilo=0 ihi=-1. What is your hardware and Fortran compiler? I'm using Intel Fortran 8.1 EMT64 and gcc3 to build the code. I had same experience (but for different GAMESS example, exam36), after upgrading Linux on my Opteron cluster to CentOS 4.3: with old Linux it did worked, but not with the new one. I believe something changed in the system libraries. Switching to the "old" DDI helped to fix it. (But one needs to correct the underscores in ddisoc.c defines) -- Grigory Shamov, Kazan Science Centre of RAS From owner-chemistry@ccl.net Mon May 29 07:23:00 2006 From: "RICHARD JILL WOOD rwoodphd..msn.com" To: CCL Subject: CCL: DNA modelling (missing atoms in PDB files) Message-Id: <-31853-060529072055-5663-LTI9w/B9tdIDqoIDJv3v/A]-[server.ccl.net> X-Original-From: "RICHARD JILL WOOD" Content-Type: text/plain; format=flowed Date: Mon, 29 May 2006 11:20:44 +0000 Mime-Version: 1.0 Sent to CCL by: "RICHARD JILL WOOD" [rwoodphd]|[msn.com] I'm wondering if someone can provide the instructions for installing MMTK under Windows. Richard >From: "Konrad Hinsen konrad.hinsen() cea.fr" >Reply-To: "CCL Subscribers" >To: "Wood, Richard L. " >Subject: CCL: DNA modelling (missing atoms in PDB files) >Date: Wed, 24 May 2006 10:38:41 -0400 > >Sent to CCL by: "Konrad Hinsen" [konrad.hinsen:cea.fr] >On 24.05.2006, at 14:53, Miro Moman miromoman%a%gmail.com wrote: > >I am currently modelling protein/DNA complexes. In both protein and DNA >structures there are >missing atoms/residues. For proteins, I know a number of freely avaliable >programs that "guess" >the coordinates of the non-resolved atoms and try to reconstruct the >structure accordingly (such as >SPDBV). However, I could not find any free program able to "correct" the >DNA structures in a similar >way (the only one I know is LeAP, which comes with the AMBER package). I >would very much >appreciate any information on such a program. > >The Molecular Modelling Toolkit (MMTK), available from > > http://dirac.cnrs-orleans.fr/MMTK/ > >will do this for proteins, DNA, and most other organic molecules. >*However*, it can compute >missing coordinates only for hydrogen atoms. >-- >------------------------------------------------------------------------------- >Konrad Hinsen >Laboratoire Leon Brillouin (CEA-CNRS), CEA Saclay, >91191 Gif-sur-Yvette Cedex, France >Tel.: +33-1 69 08 79 25 >Fax: +33-1 69 08 82 61 >E-Mail: konrad.hinsen[*]cea.fr >-------------------------------------------------------------------------------> > > _________________________________________________________________ Express yourself instantly with MSN Messenger! Download today - it's FREE! http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/ From owner-chemistry@ccl.net Mon May 29 10:47:00 2006 From: "tarig elshaarani mohamed shaarany_11[A]yahoo.com" To: CCL Subject: CCL:G: IRC & TS CALCULATION Message-Id: <-31854-060528084843-8398-q0C9f5tn2LtoSpUI7fbvmA**server.ccl.net> X-Original-From: "tarig elshaarani mohamed" Date: Sun, 28 May 2006 08:35:45 -0400 Sent to CCL by: "tarig elshaarani mohamed" [shaarany_11|,|yahoo.com] Dear Sir/Mme: I am a gradute student from Sudan ,working on theoretical studies of Diels_Alder reaction using G03,(following the reaction using density function theory)..my problem is that; whenever i make my (input)file by Molder and (export )it to G03 to process calculations,especially when i use IRC or TS as keywords a message pop up to me reading(insert the force constant calculations) but when i respond to this by writing(calc FC ) as key word with IRC or TS, another message pop up reading (input error)..What do you suggest i should do to overcome this?...Also is there any software that can prepare the coordinates as Z matrix?.... Thank You so much Tarig Elshaarani M.Sc student University of Khartoum -- From owner-chemistry@ccl.net Mon May 29 11:22:00 2006 From: "Tommy Ohyun Kwon ohyun.kwon===chemistry.gatech.edu" To: CCL Subject: CCL: tddft for metal complexes Message-Id: <-31855-060527100951-1858-dV52eDtOJryM05l2RRF0Xw!=!server.ccl.net> X-Original-From: Tommy Ohyun Kwon Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Sat, 27 May 2006 09:08:32 -0400 MIME-Version: 1.0 Sent to CCL by: Tommy Ohyun Kwon [ohyun.kwon.%.chemistry.gatech.edu] Dear CCLers; I would like to know which densify functional gives good excitation energies of transition metal complexes, especially Pt complexes. Any advice and reference would be greatly appreciated. Have a good weekend! Best wishes, Tommy -- Tommy Ohyun Kwon, Ph.D School of Chemistry and Biochemistry Georgia Institute of Technology Atlanta Georgia, 30332 Email: ohyun.kwon%chemistry.gatech.edu From owner-chemistry@ccl.net Mon May 29 11:57:01 2006 From: "Jim Kress ccl_nospam|*|kressworks.com" To: CCL Subject: CCL:G: IRC & TS CALCULATION Message-Id: <-31856-060529113326-10082-IwfayYlrblGNboM+Qls+ag- -server.ccl.net> X-Original-From: "Jim Kress" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Mon, 29 May 2006 11:32:40 -0400 MIME-Version: 1.0 Sent to CCL by: "Jim Kress" [ccl_nospam]![kressworks.com] I would suggest you make sure you have a legal copy of the software, which should include a copy of the user's manual, and then read the manual. Then, if you still can't get the calculation to work, come back to the list. Also, NEVER depend on 3rd party programs to generate completely accurate input files for Gaussian, GAMESS or any other program. 3rd party programs ALWAYS have limitations on what and how options they will specify . Jim > -----Original Message----- > From: tarig elshaarani mohamed shaarany_11[A]yahoo.com > [mailto:owner-chemistry^ccl.net] > Sent: Monday, May 29, 2006 10:53 AM > To: Kress, Jim > Subject: CCL:G: IRC & TS CALCULATION > > Sent to CCL by: "tarig elshaarani mohamed" [shaarany_11|,|yahoo.com] > > Dear Sir/Mme: > > I am a gradute student from Sudan ,working on theoretical > studies of Diels_Alder reaction using G03,(following the > reaction using density function theory)..my problem is that; > whenever i make my (input)file by Molder and (export )it to > G03 to process calculations,especially when i use IRC or TS > as keywords a message pop up to me reading(insert the force > constant calculations) but when i respond to this by > writing(calc FC ) as key word with IRC or TS, another > message pop up reading (input error)..What do you suggest i > should do to overcome this?...Also is there any software that > can prepare the coordinates as Z matrix?.... > > > > > > > > Thank You so much > > Tarig Elshaarani > M.Sc student > University of Khartoum > > > -- > > > > -= This is automatically added to each message by the mailing > script =- > To recover the email address of the author of the message, > please change> Conferences: > http://server.ccl.net/chemistry/announcements/conferences/ > > Search Messages: http://www.ccl.net/htdig (login: ccl, > Password: search)> > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > -+-+-+-+-+ > > > > > > From owner-chemistry@ccl.net Mon May 29 12:32:00 2006 From: "Luca Bertini luca.bertini[A]istm.cnr.it" To: CCL Subject: CCL: tddft for metal complexes Message-Id: <-31857-060529113821-13818-GK4I6qI88Tzaqh6Caabf/A],[server.ccl.net> X-Original-From: "Luca Bertini" Content-Type: text/plain; charset=iso-8859-1 Date: Mon, 29 May 2006 17:38:11 +0200 MIME-Version: 1.0 Sent to CCL by: "Luca Bertini" [luca.bertini(!)istm.cnr.it] Hi Tommy, As far as I know, there is not a safe recipe for excitation energies, as for the computation of the ground state properties. In the recent literature you can find some paper about this issue. The most recent one (I guess...) is J. Chem. Theory Comput. 1, 953-962 (2005). Check it out! In any case, I would always recommend to computed excitation energies with different DFT funtionals, in order to understand which is the best one for your systems. Best, Luca B. ---------- Original Message ----------- > From: "Tommy Ohyun Kwon ohyun.kwon===chemistry.gatech.edu" To: "Bertini, Luca " Sent: Mon, 29 May 2006 11:25:56 -0400 Subject: CCL: tddft for metal complexes > Sent to CCL by: Tommy Ohyun Kwon [ohyun.kwon.^.chemistry.gatech.edu] > > Dear CCLers; > I would like to know which densify functional gives good excitation energies > of transition metal complexes, especially Pt complexes. > Any advice and reference would be greatly appreciated. > Have a good weekend! > > Best wishes, > > Tommy > > -- > Tommy Ohyun Kwon, Ph.D > School of Chemistry and Biochemistry > Georgia Institute of Technology > Atlanta Georgia, 30332 > Email: ohyun.kwon^-^chemistry.gatech.edu > > -= 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> > Search Messages: http://www.ccl.net/htdig (login: ccl, Password: > search)> > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+- > +-+ ------- End of Original Message ------- From owner-chemistry@ccl.net Mon May 29 13:06:00 2006 From: "Nuno A. G. Bandeira nuno.bandeira]![ist.utl.pt" To: CCL Subject: CCL: tddft for metal complexes Message-Id: <-31858-060529122324-2962-z0lVAhkLMUy769J+MWtl3g:server.ccl.net> X-Original-From: "Nuno A. G. Bandeira" Date: Mon, 29 May 2006 12:23:20 -0400 Sent to CCL by: "Nuno A. G. Bandeira" [nuno.bandeira.:.ist.utl.pt] Tommy Ohyun Kwon ohyun.kwon===chemistry.gatech.edu wrote: > Sent to CCL by: Tommy Ohyun Kwon [ohyun.kwon.---.chemistry.gatech.edu] > > > Dear CCLers; > I would like to know which densify functional gives good excitation energies > of transition metal complexes, especially Pt complexes. > Any advice and reference would be greatly appreciated. > Have a good weekend! Any one of these functionals are known to be fairly accurate for such tasks: B3LYP, BP86, PW91 I don't know which software you use but if you're looking to trace high lying excitation energies you should use special assymptotic potentials like LB94 or CS00. -- 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 Mon May 29 13:41:00 2006 From: "=?ISO-8859-1?Q?Jordi_Vill=E0_i_Freixa?= jvilla-#-imim.es" To: CCL Subject: CCL:G: IRC & TS CALCULATION Message-Id: <-31859-060529130917-7021-9iEjMjaij080FCm5aG+sUA(0)server.ccl.net> X-Original-From: =?ISO-8859-1?Q?Jordi_Vill=E0_i_Freixa?= Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Mon, 29 May 2006 19:09:06 +0200 MIME-Version: 1.0 Sent to CCL by: =?ISO-8859-1?Q?Jordi_Vill=E0_i_Freixa?= [jvilla]~[imim.es] Dear Tarig, as surely you must be in the situation of having lost the manual, waiting for a replacement from Gaussian Inc., have a look at the web page that the Gaussian people have kindly included in the web, to help in such cases. (http://www.gaussian.com/g_ur/g03mantop.htm) I am sorry but personally I try to avoid propietary software because of these inconvenient situations since some time ago, but perhaps some other people can help you sending you example scripts to fix your problem. I wish you luck Jordi En/na Jim Kress ccl_nospam|*|kressworks.com ha escrit: > Sent to CCL by: "Jim Kress" [ccl_nospam]![kressworks.com] > I would suggest you make sure you have a legal copy of the software, which > should include a copy of the user's manual, and then read the manual. Then, > if you still can't get the calculation to work, come back to the list. > > Also, NEVER depend on 3rd party programs to generate completely accurate > input files for Gaussian, GAMESS or any other program. 3rd party programs > ALWAYS have limitations on what and how options they will specify . > > Jim > > >> -----Original Message----- >> From: tarig elshaarani mohamed shaarany_11[A]yahoo.com >> [mailto:owner-chemistry ~~ ccl.net] >> Sent: Monday, May 29, 2006 10:53 AM >> To: Kress, Jim >> Subject: CCL:G: IRC & TS CALCULATION >> >> Sent to CCL by: "tarig elshaarani mohamed" [shaarany_11|,|yahoo.com] >> >> Dear Sir/Mme: >> >> I am a gradute student from Sudan ,working on theoretical >> studies of Diels_Alder reaction using G03,(following the >> reaction using density function theory)..my problem is that; >> whenever i make my (input)file by Molder and (export )it to >> G03 to process calculations,especially when i use IRC or TS >> as keywords a message pop up to me reading(insert the force >> constant calculations) but when i respond to this by >> writing(calc FC ) as key word with IRC or TS, another >> message pop up reading (input error)..What do you suggest i >> should do to overcome this?...Also is there any software that >> can prepare the coordinates as Z matrix?.... >> >> >> >> >> >> >> >> Thank You so much >> >> Tarig Elshaarani >> M.Sc student >> University of Khartoum >> >> >> -- >> >> >> >> -= This is automatically added to each message by the mailing >> script =- >> To recover the email address of the author of the message, >> please change> Conferences: >> http://server.ccl.net/chemistry/announcements/conferences/ >> >> Search Messages: http://www.ccl.net/htdig (login: ccl, >> Password: search)> >> -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ >> -+-+-+-+-+> > > > > -- Jordi Villà i Freixa Computational Biochemistry and Biophysics lab Research Group on Biomedical Informatics (GRIB) - IMIM/UPF C/ Doctor Aiguader, 80; 08003 Barcelona (Spain) Tel: +34 93 221 1009 ext 2619 // Fax: +34 93 221 3237 e-mail: jvilla . imim.es http://diana.imim.es MSc on Bioinformatics for Health Sciences http://diana.imim.es/mbio http://www.idec.upf.edu/mbio From owner-chemistry@ccl.net Mon May 29 14:58:00 2006 From: "Satyender Goel sgoel(_)mail.ucf.edu" To: CCL Subject: CCL: Equilibration run in MD simulations of metal clusters Message-Id: <-31860-060529142616-10372-8MzMIlREH3k/lgHp7S+nCA-#-server.ccl.net> X-Original-From: "Satyender Goel" Date: Mon, 29 May 2006 14:26:14 -0400 Sent to CCL by: "Satyender Goel" [sgoel===mail.ucf.edu] Hi I am working on Molecular Dynamic Simulation of Metal Clusters to study their melting behaviour. I am using Lammps to carry out the simulations under NVT and NVE conditions. Before going for production run I am doing an Equilibration run for 200ps to 600ps with a time step of 1fs. I have few queries regarding equilibration: 1. How to decide that system has come to equilibrium and production run could be started. 2. What all parameters could be studied to see equilibrium state under NVT/NVE. Thanks for help, Regards, Satyender Goel Research Assistant, NSTC,UCF Email: Sgoel|-|mail.ucf.edu From owner-chemistry@ccl.net Mon May 29 16:54:01 2006 From: "Konrad Hinsen konrad.hinsen-$-cea.fr" To: CCL Subject: CCL: DNA modelling (missing atoms in PDB files) Message-Id: <-31861-060529152600-4752-zW95GSHmqSYjdt5f1Jy4+Q.@.server.ccl.net> X-Original-From: "Konrad Hinsen" Date: Mon, 29 May 2006 15:25:58 -0400 Sent to CCL by: "Konrad Hinsen" [konrad.hinsen{:}cea.fr] On 29.05.2006, at 13:33, RICHARD JILL WOOD rwoodphd..msn.com wrote: > I'm wondering if someone can provide the instructions for installing MMTK > under Windows. You can download a Windows binary installer from http://sourcesup.cru.fr/projects/mmtk/ If you want to compile MMTK yourself (e.g. because you want to use the development version, or a different Python release), then I can't help you directly, because I do not use Windows myself. However, the standard installation procedure for Python packages should work, and there are Windows users on the MMTK mailing list (http://starship.python.net/mailman/listinfo/mmtk) that can help you with the procedure. -- ------------------------------------------------------------------------------- Konrad Hinsen Laboratoire Leon Brillouin (CEA-CNRS), CEA Saclay, 91191 Gif-sur-Yvette Cedex, France Tel.: +33-1 69 08 79 25 Fax: +33-1 69 08 82 61 E-Mail: konrad.hinsen:_:cea.fr ------------------------------------------------------------------------------- From owner-chemistry@ccl.net Mon May 29 18:41:00 2006 From: "Gilles Frapper gilles.frapper()univ-poitiers.fr" To: CCL Subject: CCL: metal-carbon open-shell systems Message-Id: <-31862-060529144046-14634-duF2962qkoC5EMj4GI9nTw(!)server.ccl.net> X-Original-From: Gilles Frapper Content-Type: multipart/alternative; boundary="------------060903060901010405020005" Date: Mon, 29 May 2006 19:05:29 +0200 MIME-Version: 1.0 Sent to CCL by: Gilles Frapper [gilles.frapper() univ-poitiers.fr] This is a multi-part message in MIME format. --------------060903060901010405020005 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 8bit Dear all, le bonjour ! Looking at the following reaction : M(g) + C6H6 = M(eta6-C6H6) with M = Sc to Ni, I try to evaluate the reaction energy. This system is a molecular model for metal/hydrogen adsorption on graphite/nanotube ; we did already calculations using periodic models and VASP program ; PW91, plane waves). I used B3LYP, XLYP (Handy) and BPW91 with SDD or Lanl2DZ for M and 6-31G(d,p) for C,H or 6-311g(d,p) for M, C, H. Results are crazy: the deltaE is running in a range of 0-2 eV for the same system (eg Ti). [The electronic state is double-checked]. So, I try to look at the first exited state of a single metal atom in order to evaluate the dn/4s2 -> d(n+1)4s1 transition energy in order to get a way to chose the method (functional /vs. /hybrid, full basis /vs./ ecp, ...). The results are still crazy. As I have a lot of calculations to do, *what should be the cheapest way in evaluating this kind of bonding energy (adsorption energy) M+Bz = M(eta6-Bz)? * *Do you have any references ?* (Several papers have been published on this subject : DelBruno, Pandey, ... but no systematic study has been done as far as we know and, for periodic system, the PW91 functional is used but I feel that this functional is not adapted for such open-shell systems). [The "multireference character" of these open-shell systems seems to play a crucial role. _I can not used casscf+mp2 method_, ok ;-) Aubert-Frecon et al. conclude that M(Bz) are metastable molecules ... ; the long-range M---Bz system - 3/4 Ang. apart, is more stable by more than 1 eV than the short-range one ... CASSCF-MRCI calc. in chem. phys. lett, 2005, p. 422]. Best regards, Gilles -- Gilles Frapper groupe chimie quantique appliquée UMR CNRS 6503 - LACCO - Université de Poitiers 40, av. recteur Pineau 86022 Poitiers cedex tel : 05 49 45 35 74 - mel : gilles.frapper**univ-poitiers.fr site : http://labo.univ-poitiers.fr/yargla --------------060903060901010405020005 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Dear all, le bonjour !

Looking at the following reaction :
M(g) + C6H6 = M(eta6-C6H6)  with M = Sc to Ni, I try to evaluate the reaction energy. 

This system is a molecular model for metal/hydrogen adsorption on graphite/nanotube ; we did already calculations using periodic models and VASP program ; PW91, plane waves).

I used B3LYP, XLYP (Handy) and BPW91 with SDD or Lanl2DZ for M and 6-31G(d,p) for C,H or 6-311g(d,p) for M, C, H.

Results are crazy: the deltaE is running in a range of 0-2 eV for the same system (eg Ti). [The electronic state is double-checked].

So, I try to look at the first exited state of a single metal atom in order to evaluate the dn/4s2 -> d(n+1)4s1 transition energy in order to get a way to chose the method (functional vs. hybrid,  full basis vs. ecp, ...).
The results are still crazy.


As I have a lot of calculations to do,
what should be the cheapest way in evaluating this kind of bonding energy (adsorption energy) M+Bz = M(eta6-Bz)?

Do you have any references ? (Several papers have been published on this subject : DelBruno, Pandey, ... but no systematic study has been done as far as we know and, for periodic system, the PW91 functional is used but I feel that this functional is not adapted for such open-shell systems).

[The "multireference character" of these open-shell systems seems to play a crucial role.
I can not used casscf+mp2 method, ok ;-)  
Aubert-Frecon et al. conclude that M(Bz) are metastable molecules ...  ; the long-range M---Bz system - 3/4 Ang. apart,  is more stable by more than 1 eV than the short-range one ... CASSCF-MRCI  calc.
in chem. phys. lett, 2005, p. 422].


Best regards,

Gilles

 
-- 
Gilles Frapper
groupe chimie quantique appliquée
UMR CNRS 6503 - LACCO - Université de Poitiers
40, av. recteur Pineau 86022 Poitiers cedex
tel : 05 49 45 35 74 - mel : gilles.frapper**univ-poitiers.fr
site : http://labo.univ-poitiers.fr/yargla
--------------060903060901010405020005--