[gmx-users] Umbrella Sampling tutorial by Dr. Justin Lemkul

Justin Lemkul jalemkul at vt.edu
Mon Oct 27 01:20:28 CET 2014

On 10/26/14 4:32 PM, Agnivo Gosai wrote:
> Dear Users
> I am following the Umbrella Sampling tutorial by Dr. Lemkul and would like
> to have one of my doubts addressed :-
> After using pdb2gmx on the supplied pdb file , a topology file is obtained
> specifying the topology files for different protein chains in .itp format..
> Inside the .itp files the inclusion of a "position restraint file" is also
> specified as follows :-
> ; Include Position restraint file
> #ifdef POSRES
> #include "posre_Protein_chain_B.itp"
> #endif
> And lastly there are .itp format position restraint files for each of the
> protein chains.
> In the tutorial it is stated that :
> Modify topol_Protein_chain_B.itp to include the following lines (at the end
> of the file):
> #ifdef POSRES_B
> #include "posre_Protein_chain_B.itp"
> #endif
> My question is :-
> Should I modify POSRES as POSRES_B or should I keep both portions by
> including the new lines at the end?

Add a new #ifdef block.  You will see the convenience of restraining all protein 
chains or just one selectively as you do the tutorial.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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