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

[John Degenstein]

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.

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

Thanks,
John Degenstein

On Fri, Jun 19, 2015 at 11:06 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 6/19/15 1:35 PM, John Degenstein wrote:
>
>> Hello,
>>
>> I am trying to build a bigger liquid phase (1000) from a small cluster of
>> molecules (125). So far I have succeeded in forming the small cluster of
>> 125 molecules shown in the below image. This was after running gmx trjconv
>> ... -pbc cluster -center to bring the molecules into the middle of the
>> box.
>>
>> http://i.imgur.com/nlgDUzh.png
>>
>> Now, the seemingly very trivial issue I am having is that I cannot figure
>> out how to remove the empty space surrounding the cluster. I would like to
>> do this automatically rather than by manually specifying a box size. Can
>> anyone suggest a workflow for doing this?
>>
>>
> Determining the box size from maximum and minimum coordinates along each
> axis should be simple from the coordinate file, otherwise apply a position
> restraint and run a couple of steps of NPT and the box will shrink down to
> fit the system.
>
> -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
>
> ==================================================
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>