[gmx-users] position restrains while pull simulation

[Justin Lemkul]

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

==================================================