[gmx-users] Nitrile_Butadiene_Rubber simulation using Gromos96

C. Batistakis cbatiss at yahoo.gr
Thu Jul 8 10:30:39 CEST 2010

Dear Mark

Many thanks


--- 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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