[gmx-users] position restrains while pull simulation

[Justin Lemkul]

On 9/27/14 12:39 PM, shivangi nangia wrote:
> Thanks Tsjerk and Justin.
>
> I have a follow up question.
>
> To generate separate restraint .itp file for popc and cardiolipin.
>
> genrestr_mpi -f 1shortmd.gro -o posre_card.itp -n 1indexsys.ndx
> genrestr_mpi -f 1shortmd.gro -o posre_popc.itp -n 1indexsys.ndx
>
> Then, I tried 2 approaches:
>
> A) Include the separate posre_popc.itp and posre_card.itp at the end of the
> respective .itp files as:
> #ifdef POSRES
> #include "posre_card.itp"
> #endif
>
> #ifdef POSRES
> #include "posre_popc.itp"
> #endif
>
> And, included define = -DPOSRES in the .mdp file.
>
>
>
> B) To include individual restraint files in the top file, as suggested by
> Justin in the link:
> http://www.gromacs.org/Documentation/Errors#Atom_index_n_in_position_restraints_out_of_bounds
>
> #include "martini_v2.P.itp"
> #include "my_martini_v2.0_lipids.itp"
> #ifdef POSRES
> #include "posre_popc.itp"
> #endif
> #include "Protein_X.itp"
> #include "my_cardio-1.itp"
> #ifdef POSRES
> #include "posre_card.itp"
> #endif
> #include "martini_v2.0_ions.itp"
> #define RUBBER_BANDS
>
> And, included define = -DPOSRES in the .mdp file
>
>
>
> I get error in both the approaches.
>

Well, what's the error?  The "out of bounds" error?  As the help text in 
genrestr tells you, "genrestr will only produce a useful file for the first 
molecule," so if you're trying to process multiple molecules at any point, it 
will fail.  Generate a posre.itp file from a coordinate file of a single 
molecule, one that is numbered from 1 and does not use global atom numbering.

-Justin

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

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
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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