[gmx-users] Position restraints

[Justin Lemkul]

On 2/24/14, 4:22 AM, davhak wrote:
> Dear All,
>
> I try to restrain the movement of a certain particle in all cholesterol
> molecules (coarse-grained model) in Z direction. To do this I add a [
> position_restraints ] section under the [ moleculetype ] of cholesterol itp
> file like:
>
> [moleculetype]
>    CHOL 		1
> ...
>
> [ position_restraints ]
> ;  i funct       fcx        fcy        fcz
> 8    1          0          0       100000
>
> The problem is that during the simulation the restrained atoms already after
> a few hundred ns move by ~0.2 nm in average.  No matter whether the
> restraining force constant is set to 100000 0r 1000. The log file shows that
> the restraining energy varies around 300-500 kJ/mol regardless of the
> restraining force constant value (there are over 200 cholesterol molecules
> in the system).
>
> As expected one gets the same outcome when the position restraint is applied
> according to the Gromacs manual i.e. by setting a define in the mdp file and
> including a separate position_restraints] itp file within an #ifdef #endif
> clause right after the inclusion of the cholesterol itp file.
>
> It should be something trivial missing in my understanding of how position
> restraint should be applied.
>

A restraint is an applied bias to disfavor some behavior, not completely prevent 
it.  A net movement of 0.2 nm over hundreds of ns is not particularly large.

-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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