[gmx-users] All bulk is moving during Umbrella sampling

[Justin Lemkul]

On 6/4/15 10:43 AM, gozde ergin wrote:
> Hi all,
>
> I am doing some umbrella sampling simulation in order to estimate the PMF
> profile of the system.
> While doing this simulations I did:
>
> -- Simulated the system in x*y*z box.
> -- In order to have a gas phase I expanded the z coordinate to 5z and
> simulate the system in x*y*5z
> -- Minimization
> -- Equilibration
> -- Pulling
> -- Than umbrella sampling.
>
> During the umbrella sampling all of bulk molecules moved on z direction.
> However the distances between the COM of pulled molecule and COM of mass
> stays constant. It is not a big problem for estimating the PMF but it is a
> problem when I want to calculate the pressure and density profile of the
> system.
>
> Do you have any suggestion to prevent the bulk molecules moving inside the
> box?
>

Use a flat-bottom restraint to confine the bulk to one region of the box. 
Otherwise, they will naturally have a tendency to fill up the available space.

-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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