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<div>I like the fit progressive sometimes more...</div>
<div> </div>
<div>Stephan</div>
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<div style="margin:0 0 10px 0;"><b>Gesendet:</b> Dienstag, 26. August 2014 um 21:49 Uhr<br/>
<b>Von:</b> "Tsjerk Wassenaar" <tsjerkw@gmail.com><br/>
<b>An:</b> "Discussion list for GROMACS users" <gmx-users@gromacs.org><br/>
<b>Betreff:</b> Re: [gmx-users] centering with trjconv</div>
<div name="quoted-content">Hey :)<br/>
<br/>
What about -pbc nojump -center ?<br/>
<br/>
Cheers,<br/>
<br/>
Tsjerk<br/>
<br/>
<br/>
On Tue, Aug 26, 2014 at 8:12 PM, Justin Lemkul <jalemkul@vt.edu> wrote:<br/>
<br/>
><br/>
><br/>
> On 8/26/14, 12:30 PM, Eric Smoll wrote:<br/>
><br/>
>> Hello GROMACS users,<br/>
>><br/>
>> I have created an infinite liquid film system by building a slab of<br/>
>> molecules in a 3D periodic unit cell where two dimensions of the film (x<br/>
>> and y) extend out to the edge of the unit cell and one (z) does not.<br/>
>><br/>
>> I found the slab drifts along the z-dimension during MD and I am trying to<br/>
>> post-process the trajectories to anchor the slab in the center of the unit<br/>
>> cell.<br/>
>><br/>
>> "trjconv -pbc mol -center -boxcenter" works well for most trajectories<br/>
>> *unless* the slab drifts so much that it comes in contact with the z<br/>
>> boundary. When this occurs, "trjconv -pbc mol -center -boxcenter" anchors<br/>
>> it in a different location. Any ideas how I can anchor the system to the<br/>
>> center of the unit cell in this situation?<br/>
>><br/>
>><br/>
> The -fit options should help here, either progressive or translation.<br/>
><br/>
> -Justin<br/>
><br/>
> --<br/>
> ==================================================<br/>
><br/>
> Justin A. Lemkul, Ph.D.<br/>
> Ruth L. Kirschstein NRSA Postdoctoral Fellow<br/>
><br/>
> Department of Pharmaceutical Sciences<br/>
> School of Pharmacy<br/>
> Health Sciences Facility II, Room 601<br/>
> University of Maryland, Baltimore<br/>
> 20 Penn St.<br/>
> Baltimore, MD 21201<br/>
><br/>
> jalemkul@outerbanks.umaryland.edu | (410) 706-7441<br/>
> <a href="http://mackerell.umaryland.edu/~jalemkul" target="_blank">http://mackerell.umaryland.edu/~jalemkul</a><br/>
><br/>
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><br/>
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--<br/>
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