[gmx-users] Problem with gmx trjconv -box -1 -1 14

[Stefano Borocci]

Hi Mark
it works. trjconv -box -1 -1 14 now change only the z dimension and
maintains the original xy value present in the xtc file.

Thanks again



                                                      Stefano


2014-09-03 14:31 GMT+02:00 Mark Abraham <mark.j.abraham at gmail.com>:

> Right - fix looks good. No need to do anything, Stefano, unless you'd like
> to grab the source code and try out the solution at
> https://gerrit.gromacs.org/#/c/3988/
>
> Mark
>
>
> On Wed, Sep 3, 2014 at 2:07 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
> >
> >
> > On 9/3/14, 7:52 AM, Mark Abraham wrote:
> >
> >> Hi,
> >>
> >> That does indeed contradict the docs. Can you please file an issue at
> >> http://redmine.gromacs.org and attach your inputs and command line, so
> we
> >> can reproduce it?
> >>
> >>
> > I think this comes from the fact that the code uses clear_mat(fr.box) and
> > then only ever reassigns fr.box[m][m] in the case of newbox[m] > 0.  If
> > it's -1, then the code does nothing to it, so it stays at zero.  Should
> be
> > a simple fix.
> >
> > -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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-- 
-----------------------------------------------
Dr Stefano Borocci
Laboratorio di Chimica e Chimica Computazionale
Dipartimento per la Innovazione nei Sistemi Biologici,
Agroalimentari e Forestali (DIBAF)
Università degli Studi della Tuscia
Largo dell'Università, snc 01100 Viterbo
Tel. +39-0761-357127
     +39-0761-357193
Fax  +39 0761-357179
e-mail: borocci at unitus.it
-----------------------------------------------