[gmx-users] trjconv index mismatch

[Juan Manuel Aceves-Hernandez]

Dear all, is there an international workshop about Gromacs in America or
Europe the near future?.


2016-04-18 17:17 GMT-05:00 Alex <nedomacho at gmail.com>:

> Hi all,
>
> I've got a system that includes a group named "CNT" consisting of 2837
> atoms. To save space, I am outputting (at a very high rate) a compressed
> trajectory that contains only that group. The GMX version is 5.0.5. Here's
> the relevant mdp excerpt:
>
>
> nstxout             =  10000
> nstcomm             =  1000
> nstxout-compressed  =  10
> compressed-x-grps   =  CNT
> nstvout             =  1000
> nstfout             =  500
> nstlog              =  100
> nstenergy           =  500
> nstlist             =  20
>
> Upon trying to convert the compressed trajectory, after selecting the
> appropriate group from the menu (CNT, 2837 atoms), I get:
>
> command: trjconv -f traj_comp.xtc -s prod.tpr -o test.pdb
>
> output:
> -------------------------------------------------------
> Program trjconv, VERSION 5.0.5
> Source code file:
> /home/smolyan/Downloads/gromacs-5.0.5/src/gromacs/gmxana/gmx_trjconv.c,
> line: 1330
>
> Fatal error:
> Index[2645] 2838 is larger than the number of atoms in the
> trajectory file (2837). There is a mismatch in the contents
> of your -f, -s and/or -n files.
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
>
> Where's this single-atom discrepancy coming from? Any suggestions?
>
> Thanks,
>
> Alex
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-- 
Juan Manuel Aceves Hernández
Laboratorio de Nanomateriales
Tel. 52 55 5623 1999 ext 39431
Tel y Fax 5623 20 68
Unidad de Investigación Multidisciplinaria
Campo 4, Facultad de Estudios Superiores Cuautitlan
Universidad Nacional Autonoma de México