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

[Justin Lemkul]

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

-- 
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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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