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

[Stefano Borocci]

Hi Justin,

I agree with you. The selection -box in trjconv create a new box and change
all the dimension; If the value is -1, the original value of dimension (from
the xtc file) is not maintained but changed to zero.

Thanks


                                                                   Stefano


2014-09-03 14:07 GMT+02:00 Justin Lemkul <jalemkul at vt.edu>:

>
>
> 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
>
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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
-----------------------------------------------