[gmx-users] Running MD on a dimeric protein
x.periole at rug.nl
Mon Aug 16 11:00:55 CEST 2010
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
> gmx-users mailing list gmx-users at gromacs.org
> Please search the archive at http://www.gromacs.org/search before
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
-------------- next part --------------
An HTML attachment was scrubbed...
More information about the gromacs.org_gmx-users