From chemistry-request ":at:" www.ccl.net Mon Sep 14 18:08:18 1998 Received: from jazz.ucc.uno.edu (jazz.ucc.uno.edu [137.30.1.6]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id SAA09696 Mon, 14 Sep 1998 18:08:16 -0400 (EDT) Received: from slater (slater.chem.uno.edu) by jazz.ucc.uno.edu (PMDF V5.1-10 #D3119) with SMTP id <01J1SYLKRWC0922GKM ^at^ jazz.ucc.uno.edu> for CHEMISTRY ^at^ www.ccl.net; Mon, 14 Sep 1998 17:06:09 CST Date: Mon, 14 Sep 1998 17:04:10 -0500 From: Howard Alper Subject: Parameterization Sender: heacm ^%at%^ jazz.ucc.uno.edu To: CHEMISTRY -x- at -x- www.ccl.net Message-id: <35FD92DA.15FB#* at *#uno.edu> Organization: University of New Orleans MIME-version: 1.0 X-Mailer: Mozilla 3.0 (X11; U; AIX 1) Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7bit Hello, Sorry if this is a repeat, but as far as I could tell this message did not post when I originally sent it (due, likely, to floods in New Orelans!) Several weeks back I wrote about parameterization and units in simulation (still waiting for some replies...) Now I have some questions about parameterization to create forcefields for MD simulations. Specifically, I am interested in parameterizing Nitromethane. While any information regarding a set of parameters (bond, angle, torsion, out-of-plane,charges,van der Waals, etc) would be welcome, we are interested in generating the neccesary parameters, and in a form suitable for use in CHARMM. To this end I have several questions: 1) I need to derive, somehow, structural parameters and force constants for bond-stretching and angle-binding. The force constants should be in units of energy/(angstroms**2) and energy/(radian**2) (I have seen some force constants in old papers that give force constants in units of millidynes/angstroms, but I do not understand how that relates to the case of angle-bending constants...) I can perform an optimization and frequency calculation in Gaussian, for example, but from what I can tell the resulting frequencies and force constants are for the normal modes of the molecule, not bonds and angles/etc. Does anyone know if Gaussian has any options to derive the type of force constants I require? Or, does anyone know of a post-Gaussian analysis program that would do the above? 2) I also need to derive van der Waals parameters. One person I asked said something on the order of "you can derive that from the interaction of two nitromethane molecules". To a parameterization novice, that is not very specific advice. Could anyone clarify what in detail needs to be done, provide references, describe how programs like Guassian might be used to get VDW parameters, etc? (If one calculates the interaction energy of two nitromethane molecules at verious distances and orientations, is not the total energy for a configuration the sum of coulombic and VDW terms? Does that mean the charges must first be derived?) Thanks in advance, Howard Alper -- Howard E. Alper, Ph.D. Dept. of Chemistry and The Advanced Materials Research Institute University of New Orleans New Orleans, LA 70148 504-280-7216 - Helping molecules find happiness for almost a 5th of a century.