[gmx-users] Creating POSRES option for MDP file

[Justin Lemkul]

On 2/27/15 8:28 PM, Agnivo Gosai wrote:
> Dear Users
>
> My system can be identified into 2 groups ( default ) namely DNA and
> Protein. To use the pull code , I want to apply pulling force on DNA and
> keep Protein fixed.
>
> Now, I have two itp files for my protein ( two chains,A and B). So do I
> need to include something like this :-
> ; Include Position restraint file
> #ifdef POSRES_P
> #include "posre_Protein_chain_A.itp"
> #endif
> and
> ; Include Position restraint file
> #ifdef POSRES_P
> #include "posre_Protein_chain_B.itp"
> #endif
>
> in both of the itp files for the two chains and then use -DPOSRES_P in the
> mdp file for the pulling simulation ?
>

The approach is correct, provided the restraint #include statements immediately 
follow the [moleculetype] directives to which they apply.

-Justin

-- 
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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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