[gmx-users] Running MD on a dimeric protein

[XAvier Periole]

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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