[gmx-users] centering with trjconv

[Eric Smoll]

Hello Tsjerk and Justin,

Thank you for the suggestions. I found the "suggested trjconv workflow" (
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions)
very helpful. I followed the workflow, including the "-pbc nojump" step and
found success.

Thank you so much for your help.

Best,
Eric


On Tue, Aug 26, 2014 at 1:49 PM, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:

> 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
> > School of Pharmacy
> > Health Sciences Facility II, Room 601
> > 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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>
> --
> Tsjerk A. Wassenaar, Ph.D.
> --
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