[gmx-users] trjconv index mismatch

Alex nedomacho at gmail.com
Tue Apr 19 00:17:54 CEST 2016

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

Program trjconv, VERSION 5.0.5
Source code file:
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?



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