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

Agnivo Gosai agnivogromacs14 at gmail.com
Sun Oct 26 21:32:32 CET 2014

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"

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"

My question is :-
Should I modify POSRES as POSRES_B or should I keep both portions by
including the new lines at the end?

Thanks & Regards
Agnivo Gosai
Grad Student, Iowa State University.

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