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

[gozde ergin]

Actually I know I need to do something like this however I don't know how
to do it.
Could anybody give a hint how this approach can be realized in GROMACS?
I could not find a clear answer in manual.

On Thu, Jun 4, 2015 at 6:38 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
>
> --
> ==================================================
>
> 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.
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>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
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