[gmx-users] Help with position restrains for heterodimer system.

Xavier Periole x.periole at rug.nl
Tue May 24 12:07:36 CEST 2005

itai bloch wrote:

>Hi everyone,
>I am trying to simulate a bilayer system with a heterodimer inside it.
>I have a problem with the position restrained stage:
>For some reason, only one of the two peptide chains remains fixed.
>I have noticed that the number of POSRES in the grompp output is
>exactly twice the number of my restrained heavy atoms (the total of
>both peptide chains).
>I have searched the GMX mailing list and tried the suggested solutions
>(i.e. ordering the molecules differently and several different
>'#include' locations), but it failed.
You need to define the posres for each molecule and thus get two files
posres_A.itp and posres_B.itp, they should be the same actually. Then 
each of them in the topology of each monomer.

You have one topol.top where you include topol_A.itp and topol._B.itp.
In each topol_?.itp you define the topology of the monomer and then put
the posres thing, like:

#ifdef POSRES
#include "posre_?.itp"

Each posres file should be defined with the numbering of the monomer alone.
(numbering begings by 1).


 Xavier Periole - Ph.D.

 Dept. of Biophysical Chemistry / MD Group   
 Univ. of Groningen
 Nijenborgh 4
 9747 AG Groningen
 The Netherlands
 Tel: +31-503634329
 Fax: +31-503634800
 email: x.periole at rug.nl
 web-page: http://md.chem.rug.nl/~periole

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