[gmx-users] multi-chain protein and position restraint simulation

Juntao Guo jguo at utk.edu
Wed Feb 12 21:37:36 CET 2003

Hi, all, I have two questions regarding multi-chain proteins and position 
restraint simulation:

1). The protein I used for simulation has several chains. It is solvated in 
SPC. The topology file generated using pdbgmx displayed this system 
[ system ]
; Name
Protein in water

[ molecules ]
; Compound        #mols
Protein_A           1
Protein_B           1
Protein_C           1
Protein_D           1
SOL              6069

In the tempaerature coupling part of the mdp file, I only used "Protein  SOL" 
for tc-grps. My question is: should I use  "Protein  SOL" or "Protein_A 
Protein_B Protein_C Protein_D SOL". I just want to make sure I did it right.

By the way, pdb2gmx has an option "-merge" which I did not use. What does it 
really do?

2): For position restraint simulation, is adding "define  = -DPOSRES" enough 
for this purpose? or we need to add the following to the topology file as 
written in the "getting started" part:

#ifdef POSRES
#include "posres_A.itp"
#include "posres_B.itp"
#include "posres_C.itp"
#include "posres_D.itp"

Thank you for your response.


More information about the gromacs.org_gmx-users mailing list