[gmx-users] centering with trjconv

[Tsjerk Wassenaar]

Hey :)

What about -pbc nojump -center ?

Cheers,

Tsjerk


On Tue, Aug 26, 2014 at 8:12 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 8/26/14, 12:30 PM, Eric Smoll wrote:
>
>> Hello GROMACS users,
>>
>> I have created an infinite liquid film system by building a slab of
>> molecules in a 3D periodic unit cell where two dimensions of the film (x
>> and y) extend out to the edge of the unit cell and one (z) does not.
>>
>> I found the slab drifts along the z-dimension during MD and I am trying to
>> post-process the trajectories to anchor the slab in the center of the unit
>> cell.
>>
>> "trjconv -pbc mol -center -boxcenter" works well for most trajectories
>> *unless* the slab drifts so much that it comes in contact with the z
>> boundary. When this occurs,  "trjconv -pbc mol -center -boxcenter" anchors
>> it in a different location. Any ideas how I can anchor the system to the
>> center of  the unit cell in this situation?
>>
>>
> The -fit options should help here, either progressive or translation.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
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> University of Maryland, Baltimore
> 20 Penn St.
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>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
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-- 
Tsjerk A. Wassenaar, Ph.D.