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
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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