[gmx-users] Nitrile_Butadiene_Rubber simulation using Gromos96
cbatiss at yahoo.gr
Thu Jul 8 10:30:39 CEST 2010
--- Στις Πέμ., 08/07/10, ο/η Mark Abraham <mark.abraham at anu.edu.au> έγραψε:
Από: Mark Abraham <mark.abraham at anu.edu.au>
Θέμα: Re: [gmx-users] Nitrile_Butadiene_Rubber simulation using Gromos96
Προς: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
Ημερομηνία: Πέμπτη, 8 Ιούλιος 2010, 4:49
----- Original Message -----
From: "C. Batistakis" <cbatiss at yahoo.gr>
Date: Wednesday, July 7, 2010 23:19
Subject: [gmx-users] Nitrile_Butadiene_Rubber simulation using Gromos96
To: gromacs <gmx-users at gromacs.org>
> Dear all > I am trying to simulate Nitrile-Butadiene-Rubber, using the Gromos96 force field.
Let the availability of suitable parameters choose the force field :-)
> I have difficulties in finding the correct parameters from the bon.itp file , in order to define the polymer in the .rtp file.
A first port of call would have been the appropriate paper for the force field - which might have made clear whether or not nitrile parameters were likely to be found.
> Can someone suggest which parameters I shall choose in the following: In Bond-stretching parameters For: 1) Triple bond between Carbon and Nitrogen (gb_????) 2) Double bond CH=CH (gb_????) In Bond-angle bending parameters For: 1) CH2-CH=CH (ga_????) 2) CH-C≡N (ga_????) In Dihedral-angle type code For: 1) CH2-CH=CH-CH2 (gd_????) 2) CH2-CH-C≡N (gd_????) > If these parameters do not exist in this force field, can you suggest me another one to use?
As a first step, try "grep nitrile *.atp" to see which of the atom type databases have nitrile in them. AMBER forcefields are probably also OK, but you'll have to install them seperately.
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