[gmx-users] position restrains while pull simulation

[shivangi nangia]

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.

Kindly guide.

Thanks,
sxn



Sat, Sep 27, 2014 at 7:37 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 9/27/14 12:10 AM, shivangi nangia wrote:
>
>> Dear gmx-users,
>>
>> I am doing a pull simulation in CG MARTINI and following the tutorial:
>> http://bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-
>> tutorials/umbrella/05_pull.html
>>
>>
>> My systems contains POPC and cardiolipin (grouped as Lipid in index file),
>> protein, water and ions.
>>
>> I want to position restrain the Lipid.
>>
>> I used genrestr to create an .itp for the lipid (both popc and cardiolipin
>> combined)
>>
>>
> This won't work, at least not as intended.  Position restraints are
> applied per [moleculetype], so you need to create individual restraint .itp
> files for each lipid.  See example at http://www.gromacs.org/
> Documentation/Errors#Atom_index_n_in_position_restraints_out_of_bounds
>
>  I included the following at the end of both cardiolipin and popc
>> respective
>> .itp files:
>> #ifdef POSRES_POPC_CARD
>> #include "posre_popc_card.itp"
>> #endif
>>
>> In my .mdp file I included:
>> define = -DPOSRES_popc_card
>>
>> I was able to successfully compile and generate .tpr file to do the pull
>> simulations.
>>
>>
> grompp succeeds because the capitalization of the #ifdef and the define
> statement don't match, so the restraints aren't invoked.  If they were,
> they would certainly give rise to a fatal error.
>
> -Justin
>
>  I noticed that after the pull, the lipid beads are also getting
>> "drained/stretched" along with the protein.
>>
>> Could you please guide as to why this may be happening even though I have
>> the restrains on.
>>
>>
>> Kindly help.
>>
>>
>> Thanks,
>> sxn
>>
>>
> --
> ==================================================
>
> 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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