[gmx-users] mapping indices in posre/topol files to those in index files

[Justin Lemkul]

On 7/25/16 5:04 PM, Irem Altan wrote:
> Thank you for your reply. They don’t have to be applied identically to each chain, though. How would I solve the problem in this case?
>

Conditionally, in whatever way you choose, e.g.:

#include "topol_Protein_chain_A.itp"

#ifdef POSRES
#include "posre_Protein_chain_A.itp"
#endif

#ifdef POSRES_SPECIAL
#include "special_posre_Protein_chain_A.itp"
#endif

#ifdef POSRES_DIFFERENT
#include "some_other_special_posre_Protein_chain_A.itp"
#endif

etc.

You can apply one or more of these simultaneously, for any chain, using "define" 
in the .mdp file.

-Justin

-- 
==================================================

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
http://mackerell.umaryland.edu/~jalemkul

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