[gmx-users] Running MD on a dimeric protein

[Justin A. Lemkul]

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
> <http://sigads.rediff.com/RealMedia/ads/click_nx.ads/www.rediffmail.com/signatureline.htm@Middle?>
> 

-- 
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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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