[gmx-users] Running MD on a dimeric protein

[Mark Abraham]

----- Original Message -----
From: onetwo  <twoone21 at rediffmail.com>
Date: Monday, August 16, 2010 18:55
Subject: [gmx-users] Running MD on a dimeric protein
To: gmx-users at gromacs.org

> 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.

 The GROMACS index groups (of which tc-grps are perhaps the most commonly used, see manual for more info) are either provided to grompp via a file supplied with the -n parameter, or (in its absence) automatically generated by grompp. Either way, its output should provide enough clues to work out what has been regarded as Protein (e.g. residue or atom count). In extremis, you can use gmxdump on the .tpr to see the contents of the groups.

Unless you've gone out of your way to break things (e.g. changed the database of amino acid atom names), the default index groups generated by grompp will regard both your dimer parts as Protein.

If the dimer parts are adjacent, then tc-grps of Protein and Non-Protein are probably best. If they're apart, then you may want to couple the two parts separately. See http://www.gromacs.org/Documentation/Terminology/Thermostats in the first instance.

Mark

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