[gmx-users] Re: Actual box size

Justin Lemkul jalemkul at vt.edu
Tue Dec 18 19:48:45 CET 2012

On 12/18/12 1:44 PM, zugunder wrote:
> Justin Lemkul wrote
>> You need a .tpr file and can re-wrap the periodic image with trjconv -pbc
>> mol -ur compact.
> Funny, it needs a file which I don't find:
> g_trjconv -f nvt_minimized.trr -o nvt_minimized_compact.xtc -pbc mol -ur
> compact
> Program g_trjconv, VERSION 4.5.5
> Source code file: /builddir/build/BUILD/gromacs-4.5.5/src/gmxlib/gmxfio.c,
> line: 519
> Can not open file:
> topol.tpr
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors

If you don't specify an actual file name to -s, then all Gromacs tools look for 
a default file name, which in this case is "topol.tpr."  Since you've run a 
simulation, clearly you have a .tpr file, which is what you need to provide to -s.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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