From mathieu@ripault.cea.fr Wed Mar 18 02:18:32 1998 Received: from nenuphar.saclay.cea.fr for mathieu@ripault.cea.fr by www.ccl.net (8.8.3/950822.1) id CAA00119; Wed, 18 Mar 1998 02:03:15 -0500 (EST) Received: from muguet.saclay.cea.fr (muguet.saclay.cea.fr [132.166.192.6]) by nenuphar.saclay.cea.fr (8.8.8/CEAnet-relay-4.0.3) with ESMTP id IAA15129 for ; Wed, 18 Mar 1998 08:03:10 +0100 (MET) Received: from cerbere.limeil.cea.fr (cerbere.bruyeres.cea.fr [132.165.76.1]) by muguet.saclay.cea.fr (8.8.8/CEAnet-relay-4.0.3) with SMTP id IAA13709 for ; Wed, 18 Mar 1998 08:03:09 +0100 (MET) Received: by cerbere.limeil.cea.fr (CEANET-1.1+) id AA21818; Wed, 18 Mar 1998 08:01:30 +0100 Received: from indre.ripault.cea.fr(132.165.32.1) by cerbere via smap id sma021816; Wed Mar 18 08:01:02 1998 Received: from ripault.cea.fr (cher.ripault.cea.fr [132.165.32.3]) by ripault.cea.fr. (8.8.5/8.7.3) with ESMTP id IAA13775 for ; Wed, 18 Mar 1998 08:01:35 +0100 Received: from cher.ripault.cea.fr (localhost [127.0.0.1]) by ripault.cea.fr (8.8.7/8.8.7) with SMTP id IAA00434 for ; Wed, 18 Mar 1998 08:02:12 +0100 Sender: mathieu@ripault.cea.fr Message-Id: <350F7173.107E651A@ripault.cea.fr> Date: Wed, 18 Mar 1998 07:02:11 +0000 From: Didier MATHIEU Organization: CEA - Le Ripault X-Mailer: Mozilla 3.01 (X11; I; Linux 2.0.32 i586) Mime-Version: 1.0 To: chemistry@www.ccl.net Subject: Equilibration stage in MD simulations References: <350E32DE.606503BD@ripault.cea.fr> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear all, While involved so far mostly in estimating organic materials properties >from the features of isolated molecules, I consider now carrying out condensed matter simulations in periodic boxes., for solids and liquids as well. However, with regard to non-microcanonic molecular dynamics simulations, some procedures used for equilibration are unclear to me. For instance, in J. Phys. Chem. B 101, 798-808 (1997) Sorescu, Rice and Thompson did simulations of a molecular crystal in 3 stages, which are, according to my understanding of the paper : 1. NVT simulation (4 ps) 2. NVE simulation (6 ps) 3. NPT simulation (10 ps) for each T, at P=0 with velocities scaling for the first 4 ps and averages recording for the 6 last ps. Were I to record averages in the NPT ensemble, I would naively have first equilibrated the system through NPT simulations, then I would have computed NVE trajectories to estimate averages. I think I need some advice to understand how to perform non-NVE simulations. Here are related questions : * In the abovementionned paper, averages are recordes from NPT trajectories, without velocities scaling. Therefore, how is temperature constrained ? No mention is made in the paper of any thermostat such as Nose's. * On the other hand, it is not clear to me whether it is meaningful to record averages when the equations of motion are not strictly Newton's, i.e. not in the microcanonical ensemble. For instance in the NVT ensemble it is intuitive that the average could in principle be obtained over a set of NVE trajectories with the energy E sampled in the canonical ensemble according to the temperature T. However, it is not so clear whether it is meaningful to record averages from trajectories derived from Nose's equations, for instance... Thanks to anybody which could enlight me on these subjects. Regards -- Didier MATHIEU CEA - Le Ripault, BP 16 37260 Monts (France) Tel. 33(0)2.47.34.41.85 From raji@ymail.yu.edu Wed Mar 18 12:18:37 1998 Received: from acis.mc.yu.edu for raji@ymail.yu.edu by www.ccl.net (8.8.3/950822.1) id LAA02977; Wed, 18 Mar 1998 11:58:58 -0500 (EST) Received: (from raji@localhost) by acis.mc.yu.edu (8.8.5/8.8.5) id LAA32132; Wed, 18 Mar 1998 11:57:02 -0500 Date: Wed, 18 Mar 1998 11:57:02 -0500 (EST) From: Raji Viswanathan X-Sender: raji@acis.mc.yu.edu To: chemistry@www.ccl.net Subject: Sun vs SGI - Summmary Message-ID: Organization: Yeshiva University MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII There were a number of responses to my query. I am thankful to everyone who responded. I have summarized the responses below: Almost everyone who responded favored the SGI over the sun workstations. Sun does not seem to be very active in the chemistry marketplace. Many of the computational chemistry software are not available on the sun. Raji From crwatts@creighton.edu Wed Mar 18 18:18:40 1998 Received: from mailjay.creighton.edu for crwatts@creighton.edu by www.ccl.net (8.8.3/950822.1) id SAA06916; Wed, 18 Mar 1998 18:09:37 -0500 (EST) From: Received: from bluejay.creighton.edu by mailjay.creighton.edu with SMTP (1.40.112.8/16.2) id AA095542575; Wed, 18 Mar 1998 17:09:35 -0600 Date: Wed, 18 Mar 1998 17:09:35 -0600 (CST) To: Computational Chemistry List Subject: CD Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCL members: Does anyone know of a program that is capable of calculating the CD spectra of a peptide (approx 160 atoms). Thanks From crwatts@creighton.edu Wed Mar 18 19:18:40 1998 Received: from mailjay.creighton.edu for crwatts@creighton.edu by www.ccl.net (8.8.3/950822.1) id SAA07093; Wed, 18 Mar 1998 18:27:43 -0500 (EST) From: Received: from bluejay.creighton.edu by mailjay.creighton.edu with SMTP (1.40.112.8/16.2) id AA230593664; Wed, 18 Mar 1998 17:27:44 -0600 Date: Wed, 18 Mar 1998 17:27:44 -0600 (CST) To: Computational Chemistry List Subject: Circular Dichroism Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCL Members: After rereading my message, I thought I should be a little more clear about what I want. Does anyone know of any software that can calculate the CD spectra of a peptide (approximately 160 atoms) based on its known three dimensional structure. Note, I am NOT interested in spectral deconvolution software. Thanks, Charles R. Watts Ph.D Creighton University School of Medicine 2500 California Plaza Omaha, NE 68178 phone: (402) 280-2210 e-mail: crwatts@bluejay.creighton.edu