[gmx-users] gmx check

Mark Abraham mark.j.abraham at gmail.com
Fri Jul 28 13:33:15 CEST 2017


It's hard to tell without seeing the messages and knowing whether those
bonds were constrained.


On Fri, 28 Jul 2017 13:19 Dawid das <addiw7 at googlemail.com> wrote:

> 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
> here.
> "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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