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.
Look in both topol_A.itp and topol_B.itp - you will find two separate molecules
defined.
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.
http://www.gromacs.org/Documentation/Terminology/Default_Index_Groups
-Justin
Thanks in advance
Regards
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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