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

Xavier Periole x.periole at rug.nl
Tue May 24 12:20:02 CEST 2005

Xavier Periole wrote:

> 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 
> include
> each of them in the topology of each monomer.
That is for the homodimer.For the heterodimer you got two different 
posres ...

> 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"
> #endif
> Each posres file should be defined with the numbering of the monomer 
> alone.
> (numbering begings by 1).
> XAvier

 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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