[gmx-users] Problem with position restraints£¡£¡£¡£¡£¡£¡

nanyu101 nanyu101 at sina.com
Sun Oct 19 14:49:01 CEST 2003

Dear gmx-users,
    I am doing simulation for an ion channel in lipid bilayer. Now, I want to restraint the ion channel(not a normal ion channel) for the water molecules entering the channel. I just did as follows:
1.create a  posre.itp file for my ion channel and rename it as posre_phb.itp.

2.edit the ion.top file.

;include forcefield parameters
#include "ffG43a2.itp"
#include "dpp.itp"
#ifdef POSRES
#include "posre.itp"
#include "phb.itp"
#ifdef POSRE_PHB
#include "posre_phb.itp"
#ifdef FLEX_SPC
#include "flexspc.itp"
#include "spc.itp"

3.edit the md.mdp file as define = -DPOSRE_PHB.
4. run grompp to create the tpr file.
5. run gmxdump to check the tpr file.And then,I found that the force matrix in gmxdump outfile is all zero.

      f[ 5636]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
      f[ 5637]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
So,I think my position restrain failed. After I run the dynamics, my ion channel topology was distorted just as my expectation.

Would you please give some comments? THanks a lot.

Best wishes,

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