[gmx-users] Shrink simulation box while maintaining ensemble

[Tsjerk Wassenaar]

Hi Matthias,

There is one way that I know of, but it's a bit experimental yet. If you
want to know more, you can contact me off-list.

Best,

Tsjerk

On Mon, Feb 15, 2016 at 6:17 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 2/15/16 10:35 AM, Matthias Ernst wrote:
>
>> Hi,
>>
>> I am running a protein folding simulation, starting with an extended
>> structure that needs a lot of water molecules to fulfill the minimial
>> image convenction.
>> Is there a way to "shrink" a simulation box and get rid of unnecessary
>> solvent molecules while keeping velocities (to preserve the ensemble as
>> far as possible and avoid re-equilibration)?
>>
>>
> You could define a group of atoms that satisfies some geometric criterion
> (boundaries for x,y,z) with gmx select, and use trjconv with that index
> group to save only those atoms.  Assuming you're doing this on a .trr file
> with velocities, those  would be preserved.  But the complication is that
> you then have a new box (which you have to define), which puts particles at
> new positions relative to the new boundaries, and those velocities and
> positions are not necessarily compatible with this new definition (you
> could have atoms at the new boundaries that are about to crash right into
> one another!), so you probably have to re-equilibrate, anyway.
>
> -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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>
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-- 
Tsjerk A. Wassenaar, Ph.D.