From owner-chemistry@ccl.net Wed Oct 15 02:55:01 2008 From: "Arvydas Tamulis tamulis^^^mserv.itpa.lt" To: CCL Subject: CCL: How to insert parameters for Sc, Fe and Er atoms in PM3 GAMESS-US? Message-Id: <-37913-081015015455-5919-ZkaVtlIUU8mG8nThDa7NDQ * server.ccl.net> X-Original-From: Arvydas Tamulis Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed Date: Wed, 15 Oct 2008 07:56:44 +0300 (EEST) MIME-Version: 1.0 Sent to CCL by: Arvydas Tamulis [tamulis*mserv.itpa.lt] Dear Colleagues, My PM3 calculations stopped in GAMESS-US because no available parameters for Sc, Fe and Er atoms. How to get and insert these parameters? DATA ARE NOT AVAILABLE FOR ELEMENT NO. 21 DATA ARE NOT AVAILABLE FOR ELEMENT NO. 26 DATA ARE NOT AVAILABLE FOR ELEMENT NO. 68 SOME ELEMENTS HAVE BEEN SPECIFIED FOR WHICH NO PARAMETERS ARE AVAILABLE. CALCULATION STOPPED. Best regards, Arvydas From owner-chemistry@ccl.net Wed Oct 15 03:30:01 2008 From: "Chris Howard c.k.howard{=}reading.ac.uk" To: CCL Subject: CCL: Molecular Dynamics Message-Id: <-37914-081014061208-3853-UK+IxeeK4I6oLJ1mTW0pgA%server.ccl.net> X-Original-From: Chris Howard Content-Type: text/plain; format=flowed; charset=ISO-8859-1 Date: 14 Oct 2008 10:36:31 +0100 Mime-Version: 1.0 Sent to CCL by: Chris Howard [c.k.howard(a)reading.ac.uk] Wikipedia has a very good overview of Molecular Dynamics: http://en.wikipedia.org/wiki/Molecular_dynamics Modelling crystals can be done with molecular Dynamics but be aware of the limitation on cell size (i.e., dont expect good simulations on desktop pcs above ~3000 Atoms). A good piece of software for Molecular Dynamics is DL_POLY_2: http://www.cse.scitech.ac.uk/ccg/software/DL_POLY/ I have used it to model both crystals and amorphous materials. Some general tips for Molecular Dynamics: - Your results will only be as good as the Potential you use and its parameters - A linear increase in the number of atoms tends to increase simulation time exponentially - Give alot of thought to boundary conditions!! I hope that's a good starting point. Chris On Oct 14 2008, Mahmoud Korani Abdel-Latif mkkhedr**hotmail.com wrote: > >Sent to CCL by: "Mahmoud Korani Abdel-Latif" [mkkhedr a hotmail.com] >Dear CCLers, >First, thanks in advance > > Second, I would like to do molecular simulation for some bio crystals > using CPMD program but unfortunately, it is the first time to me to make > molecular dynamics. So I need some simple available references to learn > about MD. Is it available to do molecular dynamics for crystals or not? > >What should I start with? >Thanks again. > >Best Regards> > > From owner-chemistry@ccl.net Wed Oct 15 08:52:01 2008 From: "shrin!^!umd.edu" To: CCL Subject: CCL: optimization w.r.t input geometry Message-Id: <-37915-081015020217-6385-iA0gUcbe9Ggzkc2J7w6ojg~~server.ccl.net> X-Original-From: Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii Date: Wed, 15 Oct 2008 01:26:48 -0400 (EDT) MIME-Version: 1.0 Sent to CCL by: [shrin\a/umd.edu] Dear Esteemed Colleagues, I would be extremely grateful for any light on how optimization with a constraint to an input connectivity is done. i.e., e.g let's say I want to optimize A-B-X and I want to know the energy of A-B-X, even when X-A-B is more stable, and I know optimization will ultimately lead to X-A-B. Is there any specific name for this kind of optimization?? Shrinwantu Pal ############################ Shrinwantu Pal Dept. of Chem University of Maryland College Park, MD 20742, USA ############################ From owner-chemistry@ccl.net Wed Oct 15 10:20:00 2008 From: "John McKelvey jmmckel|a|gmail.com" To: CCL Subject: CCL: How to insert parameters for Sc, Fe and Er atoms in PM3 GAMESS-US? Message-Id: <-37916-081015095256-16727-2HvhIEUMNt6hhT6fjhJV6w(_)server.ccl.net> X-Original-From: "John McKelvey" Content-Type: multipart/alternative; boundary="----=_Part_29849_15781641.1224078402895" Date: Wed, 15 Oct 2008 09:46:42 -0400 MIME-Version: 1.0 Sent to CCL by: "John McKelvey" [jmmckel%a%gmail.com] ------=_Part_29849_15781641.1224078402895 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline They probably do not exist for PM3. Try MOPAC2007.. it's free for academic groups and certain others.. Cheers! John McKelvey On Wed, Oct 15, 2008 at 12:56 AM, Arvydas Tamulis tamulis^^^mserv.itpa.lt < owner-chemistry||ccl.net> wrote: > > Sent to CCL by: Arvydas Tamulis [tamulis*mserv.itpa.lt] > Dear Colleagues, > > My PM3 calculations stopped in GAMESS-US because no available parameters > for Sc, Fe and Er atoms. > How to get and insert these parameters? > > DATA ARE NOT AVAILABLE FOR ELEMENT NO. 21 > DATA ARE NOT AVAILABLE FOR ELEMENT NO. 26 > DATA ARE NOT AVAILABLE FOR ELEMENT NO. 68 > SOME ELEMENTS HAVE BEEN SPECIFIED FOR WHICH > NO PARAMETERS ARE AVAILABLE. CALCULATION STOPPED. > > Best regards, > Arvydashttp://www.ccl.net/chemistry/sub_unsub.shtmlConferences: > http://server.ccl.net/chemistry/announcements/conferences/> > > ------=_Part_29849_15781641.1224078402895 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline
They probably do not exist for PM3.  Try MOPAC2007.. it's free for academic groups and certain others..

Cheers!

John McKelvey

On Wed, Oct 15, 2008 at 12:56 AM, Arvydas Tamulis tamulis^^^mserv.itpa.lt <owner-chemistry||ccl.net> wrote:

Sent to CCL by: Arvydas Tamulis [tamulis*mserv.itpa.lt]
Dear Colleagues,

My PM3 calculations stopped in GAMESS-US because no available parameters for Sc, Fe and Er atoms.
How to get and insert these parameters?

 DATA ARE NOT AVAILABLE FOR ELEMENT NO. 21
 DATA ARE NOT AVAILABLE FOR ELEMENT NO. 26
 DATA ARE NOT AVAILABLE FOR ELEMENT NO. 68
         SOME ELEMENTS HAVE BEEN SPECIFIED FOR WHICH
         NO PARAMETERS ARE AVAILABLE.  CALCULATION STOPPED.

Best regards,
Arvydas



E-mail to subscribers: CHEMISTRY||ccl.net or use:
    http://www.ccl.net/cgi-bin/ccl/send_ccl_message

E-mail to administrators: CHEMISTRY-REQUEST||ccl.net or use
    http://www.ccl.net/cgi-bin/ccl/send_ccl_message
http://www.ccl.net/chemistry/sub_unsub.shtml

Before posting, check wait time at: http://www.ccl.net

Job: http://www.ccl.net/jobs Conferences: http://server.ccl.net/chemistry/announcements/conferences/

Search Messages: http://www.ccl.net/htdig  (login: ccl, Password: search)
    http://www.ccl.net/spammers.txt

RTFI: http://www.ccl.net/chemistry/aboutccl/instructions/



------=_Part_29849_15781641.1224078402895-- From owner-chemistry@ccl.net Wed Oct 15 13:45:00 2008 From: "Mark Umbarger umbarger,+,fas.harvard.edu" To: CCL Subject: CCL: Disgeo and/or DGII source Message-Id: <-37917-081015124818-23232-q+XsCNBNVF1FpHkD1ICebA,+,server.ccl.net> X-Original-From: "Mark Umbarger" Date: Wed, 15 Oct 2008 12:48:14 -0400 Sent to CCL by: "Mark Umbarger" [umbarger#fas.harvard.edu] Hi All, I am wondering if anyone could point me to source code for the disgeo or dgII distance geometry implementations. I have implemented a new experimental technique to measure the distances between loci on bacterial chromosomes and would like to use distance geometry to generate an ensemble of structures from these distances. Thanks, Mark From owner-chemistry@ccl.net Wed Oct 15 14:38:00 2008 From: "Ol Ga eurisco1(a)pochta.ru" To: CCL Subject: CCL: ptimization w.r.t input geometry Message-Id: <-37918-081015143220-19204-pxGZmF0KtZr43cKDWa0zYQ..server.ccl.net> X-Original-From: "Ol Ga" Date: Wed, 15 Oct 2008 14:32:16 -0400 Sent to CCL by: "Ol Ga" [eurisco1.:.pochta.ru] Dear Shrinwantu Pal, I really want to help you, to give you a correct and concrete advice. But you didn't write the name of program which is used by you. It is important because different programs use different keywords to do constrained optimization. So, I can not help but I want to help. Sincerely, Ol Ga ps It is a copy of a private message that I sent you. I am worried that it has been directed to spam-folder. From owner-chemistry@ccl.net Wed Oct 15 16:26:00 2008 From: "Rommel Bezerra Viana rommelbv!A!yahoo.com.br" To: CCL Subject: CCL:G: Computer Configuration Message-Id: <-37919-081015154754-21007-lph1d/9M5cpjiJA+e9QFsw(!)server.ccl.net> X-Original-From: "Rommel Bezerra Viana" Date: Wed, 15 Oct 2008 15:47:51 -0400 Sent to CCL by: "Rommel Bezerra Viana" [rommelbv!A!yahoo.com.br] Dear Colleagues, Could somebody help me with the following doubt? What would it be the necessary configuration of my computer to run a CCSD(T) single point energies with aug-ccpVQZ basis set, in the Gaussian Program, for a cluster of 30 silver atoms? A computer with this configuration bellow could do it? Xeon Quad Core E5420, 2,5GHz, 12 MB LGA771 Motherboard: INTEL S5000VSA SATAR, 16GB RAM Hard disk Seagate 400GB SATA 7200 RPM 24x7 HOT SWAP. With the best regards, Rommel B. Viana From owner-chemistry@ccl.net Wed Oct 15 22:45:01 2008 From: "Mark Zottola mzottola!^!gmail.com" To: CCL Subject: CCL: Convergence Issues with QCISD Message-Id: <-37920-081015214746-31538-+gA8Eam0qFCSFnFgsNmH1Q() server.ccl.net> X-Original-From: "Mark Zottola" Content-Type: multipart/alternative; boundary="----=_Part_23623_9109252.1224121655404" Date: Wed, 15 Oct 2008 21:47:35 -0400 MIME-Version: 1.0 Sent to CCL by: "Mark Zottola" [mzottola_-_gmail.com] ------=_Part_23623_9109252.1224121655404 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline I am trying to calculate the wavefunction of a molecule at the QCISD level of theory with the 6-311+g(2d,p) basis set. I am not including triples in the calculation. However, I am not getting a converged CISD wavefunction. If this were a simple HF wavefunction convergence issue, I have strategies for solving it. But I am not sure what I can do to get this method to converge. Does anyone have suggestions for getting this wavefunction to converge? Thanks! Mark ------=_Part_23623_9109252.1224121655404 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline
I am trying to calculate the wavefunction of a molecule at the QCISD level of theory with the 6-311+g(2d,p) basis set.  I am not including triples in the calculation.  However, I am not getting a converged CISD wavefunction.  If this were a simple HF wavefunction convergence issue, I have strategies for solving it.  But I am not sure what I can do to get this method to converge. 
 
Does anyone have suggestions for getting this wavefunction to converge? 
 
Thanks!
 
 
Mark
------=_Part_23623_9109252.1224121655404-- From owner-chemistry@ccl.net Wed Oct 15 23:20:00 2008 From: "Kalju Kahn kalju_._chem.ucsb.edu" To: CCL Subject: CCL:G: Computer Configuration Message-Id: <-37921-081015210331-22603-YaXZhadrSltCN3UFOQTtwg~~server.ccl.net> X-Original-From: "Kalju Kahn" Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Wed, 15 Oct 2008 17:26:13 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: "Kalju Kahn" [kalju\a/chem.ucsb.edu] Rommel, I don't think so. This looks like an unrealistically large and expensive calculation! Even if you scale it down, say to 12 silver atoms, go with a more modest basis, say cc-pVTZ instead of aug-cc-pVQZ your 400GB hard disk will likely be a limiting factor. As an upgrade, consider a pair of 1TB disks in RAID0 (linux software raid) configuration as your scratch space. Kalju > > Sent to CCL by: "Rommel Bezerra Viana" [rommelbv!A!yahoo.com.br] > Dear Colleagues, > Could somebody help me with the following doubt? > What would it be the necessary configuration of my computer to run a > CCSD(T) single point energies with aug-ccpVQZ basis set, in the Gaussian > Program, for a cluster of 30 silver atoms? > A computer with this configuration bellow could do it? > Xeon Quad Core E5420, 2,5GHz, 12 MB LGA771 > Motherboard: INTEL S5000VSA SATAR, 16GB RAM > Hard disk Seagate 400GB SATA 7200 RPM 24x7 HOT SWAP. > > With the best regards, > Rommel B. Viana> > > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Dr. Kalju Kahn Department of Chemistry and Biochemistry UC Santa Barbara, CA 93106