[From nobody Thu Nov 14 11:53:16 2013
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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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Hello Sir,<br />
<br />
I am simulating a protein which is a homodimer, when I did pdb2gmx, it gene=
rated a topolgy file  in which there were two chain topologies for each cha=
in as :              <br />
<br />
; Include chain topologies<br />
#include "topol_A.itp"<br />
#include "topol_B.itp"       <br />
<br />
and in Compound section gave ;<br />
<br />
Compound        #mols<br />
Protein_A           1<br />
Protein_B           1<br />
<br />
I want to ask that if it will consider the system as one or two different p=
roteins.<br />
<br />
Also in production MD phase, in md.mdp file I mentioned<br />
<br />
Berendsen temperature coupling is on in two groups<br />
Tcoupl              =3D V-rescale<br />
tc-grps             =3D Protein Non-Protein<br />
tau_t               =3D 0.1     0.1<br />
ref_t               =3D 300     300<br />
<br />
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.<br />
<br />
Thanks in advance<br />
Regards<br><Table border=3D0 Width=3D644 Height=3D57 cellspacing=3D0 cellpa=
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