[gmx-users] Nitrile_Butadiene_Rubber simulation using Gromos96

[Mark Abraham]

----- 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>

-----------------------------------------------------------
|  -  -  -  <!--  /* Font Definitions */  @font-face 	{font-family:"Cambria Math"; 	panose-1:2 4 5 3 5 4 6 3 2 4; 	mso-font-charset:0; 	mso-generic-font-family:roman; 	mso-font-pitch:variable; 	mso-font-signature:-1610611985 1107304683 0 0 159 0;} @font-face 	{font-family:Calibri; 	panose-1:2 15 5 2 2 2 4 3 2 4; 	mso-font-charset:0; 	mso-generic-font-family:swiss; 	mso-font-pitch:variable; 	mso-font-signature:-1610611985 1073750139 0 0 159 0;}  /* Style Definitions */  p.MsoNormal, li.MsoNormal, div.MsoNormal 	{mso-style-unhide:no; 	mso-style-qformat:yes; 	mso-style-parent:""; 	margin-top:0in; 	margin-right:0in; 	margin-bottom:10.0pt; 	margin-left:0in; 	line-height:115%; 	mso-pagination:widow-orphan; 	font-size:11.0pt; 	font-family:"Calibri","sans-serif"; 	mso-ascii-font-family:Calibri; 	mso-ascii-theme-font:minor-latin; 	mso-fareast-font-family:Calibri; 	mso-fareast-theme-font:minor-latin; 	mso-hansi-font-family:Calibri; 	mso-hansi-theme-font:minor-latin; 	mso-bidi-font-family:"Times New Roman"; 	mso-bidi-theme-font:minor-bidi;} .MsoChpDefault 	{mso-style-type:export-only; 	mso-default-props:yes; 	mso-ascii-font-family:Calibri; 	mso-ascii-theme-font:minor-latin; 	mso-fareast-font-family:Calibri; 	mso-fareast-theme-font:minor-latin; 	mso-hansi-font-family:Calibri; 	mso-hansi-theme-font:minor-latin; 	mso-bidi-font-family:"Times New Roman"; 	mso-bidi-theme-font:minor-bidi;} .MsoPapDefault 	{mso-style-type:export-only; 	margin-bottom:10.0pt; 	line-height:115%;} @page WordSection1 	{size:8.5in 11.0in; 	margin:1.0in 1.0in 1.0in 1.0in; 	mso-header-margin:.5in; 	mso-footer-margin:.5in; 	mso-paper-source:0;} div.WordSection1 	{page:WordSection1;} -->   > 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.

Mark

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20100708/ff8e574d/attachment.html>