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

[John Degenstein]

Justin,

Thanks for the response, I have started to use pure OpenMP parallelization
which has solved the issue with DD. Somehow I missed this detail about
domain decomposition when reading about parallelization with tMPI vs OpenMP.

John

On Thu, Jun 25, 2015 at 6:39 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
>
> --
> ==================================================
>
> 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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