[gmx-users] Running MD on a dimeric protein
twoone21 at rediffmail.com
Mon Aug 16 07:13:34 CEST 2010
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
and in Compound section gave ;
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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