[gmx-users] gmx check

Dawid das addiw7 at googlemail.com
Fri Jul 28 13:19:31 CEST 2017

Dear Gromacs Users,

I get a bunch of communicates when I run
gmx check -f npt-md2.xtc -s1 npt-md2.tpr >& gmx-check2.out

saying that I get different bond lengths than they should be. Can that be
caused by only 0.001 nm precision of my results?
Also I am not exactly sure if I understand correctly what I am checking
"If both a trajectory and a .tpr <http://manual.gromacs.org/online/tpr.html>
file are given (with -s1) the program will check whether the bond lengths
defined in the tpr <http://manual.gromacs.org/online/tpr.html> file are
indeed correct in the trajectory."
If so, then what does it mean "correct" in this sentence? It is pretty
obvious that
bond lengths vary during simulation unless I constrain them.

Best wishes,
Dawid Grabarek

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