From owner-chemistry@ccl.net Fri Oct 26 05:45:01 2007 From: "Joe Kwiatkowski jk905-*-imperial.ac.uk" To: CCL Subject: CCL:G: 6-31+g* orbitals!=basis functions Message-Id: <-35489-071025132033-6244-gTFjY/jBE/pKXL9RFB0YNA]^[server.ccl.net> X-Original-From: Joe Kwiatkowski Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 25 Oct 2007 17:37:34 +0100 MIME-Version: 1.0 Sent to CCL by: Joe Kwiatkowski [jk905(_)imperial.ac.uk] Dear CCL'ers I have been running B3LYP/6-31+G* calculations on Naphthalene with G03. I am confused because the number of basis functions is 206, but 'punch=MO' only returns 205 orbitals. If I request the overlap matrix with iop(3/33=1) I see all 206 orbitals. What is going on? Any ideas? With thanks in advance, Joe -- Joe Kwiatkowski EXSS, Physics Imperial College London Prince Consort Road SW7 2BW Tel: 0207 594 6682 From owner-chemistry@ccl.net Fri Oct 26 05:59:01 2007 From: "alexandra.marques===fc.up.pt" To: CCL Subject: CCL:G: amber torsions Message-Id: <-35490-071025235027-583-s0KHZ63EKQ8rMdpmY9Yfpg(0)server.ccl.net> X-Original-From: alexandra.marques*|*fc.up.pt Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; format="flowed" Date: Fri, 26 Oct 2007 04:49:57 +0200 MIME-Version: 1.0 Sent to CCL by: alexandra.marques%x%fc.up.pt Hi I am a little bit confused about the way to specify amber torsions for =20 use with the amber (softfirst) in a oniom calculation in gaussian. In manual it is said that the amber torsions are specified this way: AmbTrs Atom-type1 A-type2 A-type3 A-type4 PO1 PO2 PO3 PO4 Mag1 Mag2 =20 Mag3 Mag4 NPaths PO1-PO4 Phase offsets Mag1...Mag4 V/2 magnitudes NPaths Number of paths (if < 0, determined on-the-fly). So for isntance, if I have the following parameters for a dihedral =20 CX-CY-CC-CZ: CX-CY-CC-CZ 1 0.850 180 -3 CX-CY-CC-CZ 1 0.940 180 -2 CX-CY-CC-CZ 1 -0.560 180 1 the way to specify this in amber is: AmbTrs CX CY CC CZ 180 180 180 0.850 0.940 -0.560 1 1 1 Is this correct? When using amber in gaussian, is it necessary to always specify the =20 torsion parameters involving new atom types or we just need to specify =20 the bond and angle parameters? Thanks Alexandra ------------------------------------------------------------------------- A FCUP utiliza o sistema open source de webmail Horde/IMP (www.horde.org) Visite: http://www.fc.up.pt/ http://info.fc.up.pt/ From owner-chemistry@ccl.net Fri Oct 26 08:43:00 2007 From: "Simon Halstead joyjoyhappyjoy * yahoo.co.uk" To: CCL Subject: CCL: MD of systems with a net charge using Ewald Message-Id: <-35491-071025232859-31466-QAfQONfEGdhTx1zgaDzgNQ : server.ccl.net> X-Original-From: "Simon Halstead" Date: Thu, 25 Oct 2007 23:28:56 -0400 Sent to CCL by: "Simon Halstead" [joyjoyhappyjoy(a)yahoo.co.uk] Dear all, I am running MD simulations on systems with either a net +1 or -1 charge using Ewald summation and dl_poly. The Ewald summation should correct for the net charge by adding a smeared charge over the cell. However, my results show a serious system size dependence for the potential energy (from the coulomb term). Does anyone know of any way to correct the energy results? Amy help would be greatly appreciated, Simon From owner-chemistry@ccl.net Fri Oct 26 10:52:00 2007 From: "Jinyao Wang wangjy::ciac.jl.cn" To: CCL Subject: CCL: help me Message-Id: <-35492-071026104742-24784-iNIp5ioffPjwO3lCiVzB6Q##server.ccl.net> X-Original-From: "Jinyao Wang" Date: Fri, 26 Oct 2007 10:47:39 -0400 Sent to CCL by: "Jinyao Wang" [wangjy[a]ciac.jl.cn] Dear CCL'er, I am trying to optimize different geometries between acetaldehyde and carbon dioxide moleculars in differernt pressures of CO2 when acetaldehyde dissolve into CO2. So I want to find some available softwares to perform it. I would appreciate if you could give me some suggestions. From owner-chemistry@ccl.net Fri Oct 26 11:26:01 2007 From: "immanuel feng feng.immanuel-$-gmail.com" To: CCL Subject: CCL: problem with nwchem 5.0 Message-Id: <-35493-071025115014-15111-3hQ1sqbLGWEkS64JajNzDQ(!)server.ccl.net> X-Original-From: "immanuel feng" Content-Type: multipart/alternative; boundary="----=_Part_895_376303.1193323584918" Date: Thu, 25 Oct 2007 22:46:24 +0800 MIME-Version: 1.0 Sent to CCL by: "immanuel feng" [feng.immanuel===gmail.com] ------=_Part_895_376303.1193323584918 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline hello everyone, I am pretty new to nwchem, now I want to perform the single point energy calculation with M05 DFT method on nwchem. My input file is below, but it said the dft_input directive is unknown. Could anyone give me some advice? Thank you so much! yesu start try charge 0 geometry C 0.000000 0.000000 0.000000 H 0.000000 0.000000 1.094223 H 1.031641 0.000000 -0.364776 H -0.515826 -0.893440 -0.364756 H -0.515854 0.893405 -0.364787 end basis * library 6-311++g(3df,3pd) end dft m05; singlet print low end task dft ------=_Part_895_376303.1193323584918 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline
hello everyone,
       I am pretty new to nwchem, now I = want to perform the single point energy calculation with M05 DFT method on = nwchem. My input file is below, but it said the dft_input directive is unkn= own. Could anyone give me some advice? Thank you so much!
 
           &nbs= p;            &= nbsp;           &nbs= p;            &= nbsp;           &nbs= p;            &= nbsp;           &nbs= p;            &= nbsp;           &nbs= p;            &= nbsp;           &nbs= p;            &= nbsp;           &nbs= p;            &= nbsp;           &nbs= p;            &= nbsp;           &nbs= p;            &= nbsp;     yesu
 
start try
 
charge 0
 
geometry
 C =     0.000000     0.000000  &nb= sp;  0.000000
 H     0.000000  &= nbsp;  0.000000     1.094223
 H  = ;   1.031641     0.000000    -= 0.364776
 H    -0.515826    -0.893440=     - 0.364756
 H    -0.515854     0.8= 93405    -0.364787
end
 
basis
* library 6-= 311++g(3df,3pd)
end
 
dft
 m05; singlet
 prin= t low
end
 
task dft
------=_Part_895_376303.1193323584918-- From owner-chemistry@ccl.net Fri Oct 26 12:07:01 2007 From: "Konrad Hinsen hinsen+/-cnrs-orleans.fr" To: CCL Subject: CCL: MD of systems with a net charge using Ewald Message-Id: <-35494-071026112256-6435-SseN4GkQA55D6nP67Fc5nw[*]server.ccl.net> X-Original-From: "Konrad Hinsen" Date: Fri, 26 Oct 2007 11:22:53 -0400 Sent to CCL by: "Konrad Hinsen" [hinsen#cnrs-orleans.fr] On Oct 26, 2007, at 5:28, Simon Halstead joyjoyhappyjoy * yahoo.co.uk wrote: > I am running MD simulations on systems with either a net +1 or -1 charge using Ewald summation > and dl_poly. The Ewald summation should correct for the net charge by adding a smeared charge > over the cell. However, my results show a serious system size dependence for the potential energy > (from the coulomb term). > Does anyone know of any way to correct the energy results? Ewald summation does indeed add a neutralizing background charge density, which makes the electrostatic energy finite. However, the energy depends on the system size. If you think that in your specific case the energy should not depend on system size, then please tell us why. -- --------------------------------------------------------------------- Konrad Hinsen Centre de Biophysique Molculaire, CNRS Orlans Synchrotron Soleil - Division Expriences Saint Aubin - BP 48 91192 Gif sur Yvette Cedex, France Tel. +33-1 69 35 97 15 E-Mail: hinsen^_^cnrs-orleans.fr --------------------------------------------------------------------- From owner-chemistry@ccl.net Fri Oct 26 12:51:01 2007 From: "Aleksandra Rudnitskaya aleksandra.rudnit001-x-umb.edu" To: CCL Subject: CCL:G: G03 problem with readisotopes Message-Id: <-35495-071025204841-21806-mfz0FcwEvghhJ6438YYXrw---server.ccl.net> X-Original-From: "Aleksandra Rudnitskaya" Date: Thu, 25 Oct 2007 20:48:37 -0400 Sent to CCL by: "Aleksandra Rudnitskaya" [aleksandra.rudnit001===umb.edu] Dear CCLers, I wanted to calculate opt and freq on water with different temperature and pressure. Input file looks following %Chk=h2o_t2 # opt freq=noraman rb3lyp/6-311++g(3df,3pd) Title 0 1 O H 1 B1 H 1 B2 2 A1 B1 0.960000 B2 0.960000 A1 109.471221 --Link1-- %chk=h2o_t2 # rb3lyp/6-311++g(3df,3pd) freq=(readfc,readisotopes) Geom=AllCheck 400.0 1.0 The error message is # rb3lyp/6-311++g(3df,3pd) freq=(readfc,readisotopes) Geom=AllCheck ------------------------------------------------------------------- 1/29=7,38=1,88=2/1; 2/40=1/2; 7/8=1,25=11/16; 99/5=2,8=2/99; ----- Title ----- Redundant internal coordinates taken from checkpoint file: h2o_t2.chk Charge = 0 Multiplicity = 1 O,0,-0.0165597067,0.,-0.0117094809 H,0,0.0205206193,0.,0.9485436833 H,0,0.9011357673,0.,-0.2968342024 Recover connectivity data from disk. WANTED A FLOATING POINT NUMBER AS INPUT. FOUND A STRING AS INPUT. Atom number 2, atomic number 1: [1] ? Error termination via Lnk1e in /usr/apps/chemistry/gaussian/G03/nbo/g03/l101.exe at Tue Oct 23 18:37:35 2007. Job cpu time: 0 days 0 hours 0 minutes 0.3 seconds. File lengths (MBytes): RWF= 13 Int= 0 D2E= 0 Chk= 10 Scr= 1 It seams G03( unix cluster) doesnt like temperature and pressure, while the same file was done on G98 (windows) . Any suggestions? how to fix it? Thanks in advance. Aleksandra From owner-chemistry@ccl.net Fri Oct 26 13:33:00 2007 From: "Jeff Hammond jeff.science**gmail.com" To: CCL Subject: CCL: problem with nwchem 5.0 Message-Id: <-35496-071026120935-6583-mDvFBOEXVmT5zj6uaZrJJg_._server.ccl.net> X-Original-From: "Jeff Hammond" Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Fri, 26 Oct 2007 11:09:24 -0500 MIME-Version: 1.0 Sent to CCL by: "Jeff Hammond" [jeff.science() gmail.com] Immanuel, Please modify the dft input block as follows: dft xc m05 print low end The singlet command is not understood in the DFT input block. In this case it is unnecessary, but you can add it to the SCF block like this: scf singlet end Section 11 of the NWChem User Manual (http://www.emsl.pnl.gov/docs/nwchem/doc/user/user.html) covers DFT. You can also find a number of examples in the $NWCHEM_TOP/QA/tests. If you may eventually want to use the m06 functions, please go here to get the necessary patch: http://www.emsl.pnl.gov/docs/nwchem/support/faq/m06.html In the future, please post questions about NWChem to nwchem-users#emsl.pnl.gov. You'll get better answers faster. Jeff From owner-chemistry@ccl.net Fri Oct 26 16:07:00 2007 From: "Jerome Kieffer jerome.Kieffer[A]terre-adelie.org" To: CCL Subject: CCL: Geometry optimization software ? Message-Id: <-35497-071026160139-1983-Y1mcJdjh87nID/ukXR2+og=server.ccl.net> X-Original-From: Jerome Kieffer Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-15 Date: Fri, 26 Oct 2007 22:03:58 +0200 Mime-Version: 1.0 Sent to CCL by: Jerome Kieffer [jerome.Kieffer(a)terre-adelie.org] On Thu, 25 Oct 2007 16:35:38 +0900 "Yangsoo Kim vsmember_+_gmail.com" wrote: > I would greatly appreciate if you could drop me a line with the name of > software showing good performance for the global geometry optimization. I am using the ConFlex code (provided in the CAChe worksuite) to generate a set of conformers before re-optimizing each of them using DFT or semi-empirical methods. Hopt this helps. --=20 J=E9r=F4me KIEFFER : http://www.terre-adelie.org