From owner-chemistry@ccl.net Tue Aug 22 00:23:00 2006 From: "Bhabani Mallik mbhabani a yahoo.com" To: CCL Subject: CCL: Frequency Correlation function Message-Id: <-32420-060821235100-20841-cXrf0+yYosJwJg32kxlvPQ[*]server.ccl.net> X-Original-From: "Bhabani Mallik" Date: Mon, 21 Aug 2006 23:50:59 -0400 Sent to CCL by: "Bhabani Mallik" [mbhabani]~[yahoo.com] Please someone help me how to calculate Frequency correlation function from a series of trajectories in various time steps.I have the co-ordinates and velocities of all atoms in various time step intervals. Help will be highly appreciated. regards, Shankar From owner-chemistry@ccl.net Tue Aug 22 00:58:00 2006 From: "Bhabani Mallik mbhabani-#-yahoo.com" To: CCL Subject: CCL:G: Frequency Correlation function Message-Id: <-32421-060821134052-21395-9TmMKF1By5VFzWHVWrPAjw(~)server.ccl.net> X-Original-From: Bhabani Mallik Content-Transfer-Encoding: 8bit Content-Type: multipart/alternative; boundary="0-1322316360-1156178449=:92421" Date: Mon, 21 Aug 2006 09:40:49 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Bhabani Mallik [mbhabani^yahoo.com] --0-1322316360-1156178449=:92421 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Can anyone help how to calculate the frequency correlation function from a series of trajectories ? "diksha dharmendra makwani diksha__iitb.ac.in" wrote: Sent to CCL by: "diksha dharmendra makwani" [diksha\a/iitb.ac.in] Hi, I am wondering if someone can help in calculating energy eigen values and eigen functions of molecule by Gaussian 03. If it is not possible than if someone can suggest me some other alternative. Thanks, Dr. Diksha Makwani diksha+/-iitb.ac.inhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt--------------------------------- How low will we go? Check out Yahoo! Messenger’s low PC-to-Phone call rates. --0-1322316360-1156178449=:92421 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Can anyone  help how to calculate the frequency correlation function
from a series of trajectories ?

"diksha dharmendra makwani diksha__iitb.ac.in" <owner-chemistry**ccl.net> wrote:
Sent to CCL by: "diksha dharmendra makwani" [diksha\a/iitb.ac.in]
Hi,

I am wondering if someone can help in calculating energy eigen values and eigen functions of molecule by Gaussian 03. If it is not possible than if someone can suggest me some other alternative.

Thanks,
Dr. Diksha Makwani
diksha+/-iitb.ac.in






How low will we go? Check out Yahoo! Messenger’s low PC-to-Phone call rates. --0-1322316360-1156178449=:92421-- From owner-chemistry@ccl.net Tue Aug 22 03:02:00 2006 From: "Arvydas Tamulis tamulis{:}mserv.itpa.lt" To: CCL Subject: CCL: Experimental stacking energies between nucleobases Message-Id: <-32422-060821110555-6329-QxTy9zUxWtebc9MxKc3/wA(_)server.ccl.net> X-Original-From: Arvydas Tamulis Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed Date: Mon, 21 Aug 2006 17:13:30 +0300 (EEST) MIME-Version: 1.0 Sent to CCL by: Arvydas Tamulis [tamulis-#-mserv.itpa.lt] Dear Colleagues, Would you please to say what are experimental stabilizing stacking interaction energies between natural nucleobases in water solvent? I have received stacking energy equal to around 100 kcal/mol using MP2/6-31+G* between guanine and cytosine in surrounded water cluster. With best regards, Arvydas Tamulis From owner-chemistry@ccl.net Tue Aug 22 03:56:00 2006 From: "Rafal Bachorz rafal.bachorz\a/chemie.uni-karlsruhe.de" To: CCL Subject: CCL: Experimental stacking energies between nucleobases Message-Id: <-32423-060822034927-23541-b5fP4fg0lCBh8g7qBI59Nw||server.ccl.net> X-Original-From: Rafal Bachorz Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="utf-8" Date: Tue, 22 Aug 2006 09:49:19 +0200 MIME-Version: 1.0 Sent to CCL by: Rafal Bachorz [rafal.bachorz~~chemie.uni-karlsruhe.de] > Would you please to say what are experimental stabilizing stacking > interaction energies between natural nucleobases in water solvent? > I have received stacking energy equal to around 100 kcal/mol using > MP2/6-31+G* between guanine and cytosine in surrounded water cluster. Dear Arvydas Tamulis, I do not know what are these values, but I can say that at MP2 level of theory you obtain stacking energies which are extremally overestimated. To get a proper picture of pi-stacked system you need to include at least contributions from CCSD level. Best regards, Rafal -- Rafal A. Bachorz Chair of Theoretical Chemistry Institute of Physical Chemistry University of Karlsruhe (TH) D-76128 Karlsruhe, Germany ------------------------------------------ Email: rafal.bachorz-$-chemie.uni-karlsruhe.de Telephone: +49-721-608 7269 ------------------------------------------ Office: Engesserstrasse 15, D-76131 Karlsruhe Building 30.45 (Chemie-Turm III), Room 620 From owner-chemistry@ccl.net Tue Aug 22 07:53:01 2006 From: "Serguei Patchkovskii ps]~[ned.sims.nrc.ca" To: CCL Subject: CCL: Analytical Gradients in the Halfelectron Method Message-Id: <-32424-060822063409-23730-fRfvDcYivai6ntHibP+3VA+*+server.ccl.net> X-Original-From: Serguei Patchkovskii Content-Type: TEXT/PLAIN; charset=US-ASCII Date: Tue, 22 Aug 2006 05:51:02 -0400 (EDT) MIME-Version: 1.0 Sent to CCL by: Serguei Patchkovskii [ps]^[ned.sims.nrc.ca] On Mon, 21 Aug 2006, Thomas Steinbrecher thomas.steinbrecher*_*physchem.uni-freiburg.de wrote: > Can anyone point me to a reference where this halfelectron > method has been implemented including correct analytical > gradients or explain to me why it can't be done? Thomas, Fast implementation of analytical energy gradients in Dewar's half-electron method is described here: S. Patchkovskii, W. Thiel Analytical first derivatives of the energy in the MNDO half-electron open-shell treatment Theoretica Chimica Acta, 93, 87-99 (1996) Because the half-electron correction term is not variational, analytical gradients require solution of coupled-perturbed Hartree-Fock equations and are not entirely trivial. Serguei From owner-chemistry@ccl.net Tue Aug 22 09:05:01 2006 From: "Wai-To Chan chan*curl.gkcl.yorku.ca" To: CCL Subject: CCL: Frequency Correlation function Message-Id: <-32425-060822090124-25159-wUbRMgAnu+JvckLBLDduzA+/-server.ccl.net> X-Original-From: Wai-To Chan Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii Date: Tue, 22 Aug 2006 09:09:19 -0400 (EDT) MIME-Version: 1.0 Sent to CCL by: Wai-To Chan [chan : curl.gkcl.yorku.ca] <<<<<<<<<< Please someone help me how to calculate Frequency correlation function from a series of trajectories in various time steps.I have the co-ordinates and velocities of all atoms in various time step intervals. Help will be highly appreciated. >>>>>>>>>>>>>>>>>>. Could you elaborate on what a 'Frequency correlation function' is? Given an ensemble of trajectories one can compute an autocorrelation functions Fourier transformation of the time correlation function would yield a spectrum. The correlation function is a velocity function not a frequency function. Just look up the list of standard molecular dynamics textbooks. A number of MD references were suggested in a recent thread. Wai-To Chan