The way you define things would work fine but if
your dimer is an homodimer only one topology is
needed. topol_A and topolo_B should be identical.
The part of the mdp file is fine.
On Aug 16, 2010, at 7:13 AM, onetwo wrote:
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
Regards
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