[gmx-users] multi-chain protein and position restraint simulation
jguo at utk.edu
Wed Feb 12 21:37:36 CET 2003
Hi, all, I have two questions regarding multi-chain proteins and position
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 ]
Protein in water
[ molecules ]
; Compound #mols
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
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:
Thank you for your response.
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