[gmx-users] Running MD on a dimeric protein

onetwo twoone21 at rediffmail.com
Mon Aug 16 07:13:20 CEST 2010

Hello Sir,

I am simulating a protein which is a homodimer, when I did pdb2gmx, it generated a topolgy file  in which there were two chain topologies for each chain as :              

; Include chain topologies
#include "topol_A.itp"
#include "topol_B.itp"       

and in Compound section gave ;

Compound        #mols
Protein_A           1
Protein_B           1

I want to ask that if it will consider the system as one or two different proteins.

Also in production MD phase, in md.mdp file I mentioned

Berendsen temperature coupling is on in two groups
Tcoupl              = V-rescale
tc-grps             = Protein Non-Protein
tau_t               = 0.1     0.1
ref_t               = 300     300

I have this doubt that as I have given tc-grps as Protein and Non-Protein, so if "Protein" will consider both the chains of the protein or not.

Thanks in advance
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