[gmx-users] centering with trjconv

[Tsjerk Wassenaar]

Hi Stephan,

Well, fine. I generally like (dark) chocolate cookies more (remember if you
visit) ;). But with PBC you need to make things whole or remove jumps
before doing anything to do with (rotational) fitting. And if the objective
is centering, having the bits in one piece without jumps is all there is to
it. The problem here was an infinite liquid film. That splits over
boundaries. A progressive fit is bound to fail in that case. -pbc whole
doesn't help much. You need to remove jumps. Then you probably want to have
your film in one box after centering. If you've rotated the system with a
fit, you're in trouble. That's why the trjconv workflow is written as it
is.

Cheers,

Tsjerk




On Wed, Aug 27, 2014 at 9:00 AM, lloyd riggs <lloyd.riggs at gmx.ch> wrote:

> I like the fit progressive sometimes more...
>
> Stephan
>
> *Gesendet:* Dienstag, 26. August 2014 um 21:49 Uhr
> *Von:* "Tsjerk Wassenaar" <tsjerkw at gmail.com>
> *An:* "Discussion list for GROMACS users" <gmx-users at gromacs.org>
> *Betreff:* Re: [gmx-users] centering with trjconv
> 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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-- 
Tsjerk A. Wassenaar, Ph.D.