[gmx-users] Building a Larger Liquid Phase - Truncate 'Vacuum'

[Justin Lemkul]

On 6/25/15 2:46 PM, John Degenstein wrote:
> Justin,
>
> Ok, so I decided to take a different path to solve this issue. Essentially,
> using the Berendsen Pcoupl the system should condense under high pressure.
> For some reason it does not seem to work very quickly at least. To get
> around this issue I running several steps of equilibration EM followed by
> NVT at 600K followed by NPT at 100bar with the Berendsen Pcoupl. I think
> using a higher temperature helps to increase the velocity of my larger
> (than water) molecules and thus improve the rate of condensation.
>
> After this I do another stage of NVT at 300K to get a new velocity
> distribution followed by NPT with Parrinello-Rahman at 1 bar. One issue I
> have faced is that too many steps with Pcoupl set to Parrinello-Rahman
> leads to the system collapsing rapidly which then causes issues with the
> number of DD cells relative to the current vs. old size of the box. To
> solve this issue I restart with a 2nd stage of Parrinello-Rahman again
> starting from the output structure of the 1st stage of Par-Rah. So far this
> seems to work well and results in a high and seemingly accurate density
> with a box that tightly surrounds the cluster.
>
> I suppose in retrospect that I could simply use a single processor which I
> think would reduce the number of DD cells and thus prevent this error.
>

Or just use OpenMP parallelization.  Any time you drastically change the size of 
the system, this will be the case.

> Does anyone have any thoughts/comments/concerns about my procedure?
>

Seems OK, just equilibrate thoroughly under the new conditions.

-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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