Hello,,
I am really thankful to Mark, Justin and XAvier for helping me to clear my
doubts.
Reply by Mark is really explainatory. I got my doubts clear.
Regards
Note: Forwarded message attached
-- Original Message --
From: "onetwo "twoon...@rediffmail.com
To: gmx-users@gromacs.org
Subject: Running MD on a dimeric protein
--- Begin Message ---
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
--- End Message ---
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