[gmx-users] gmx check

[Mark Abraham]

Hi,

Seems like the extremes of normal variation of unconstrained bonds. As gmx
help check suggests, the feature exists as a quick sanity check. The use of
"correct" is in the sense of "between sensible atom indices" rather than
suggesting that only one length is valid.

Mark

On Fri, 28 Jul 2017 14:41 Dawid das <addiw7 at googlemail.com> wrote:

> Hi,
>
> No, those bonds I get the message were not constrained and virtually in
> every frame there is different
> bunch of bonds for which I get this message. Because the whole output from
> gmx check is 1.1 GB,
> I just give you a few examples.
>
> Reading frame       0 time    0.000
> # Atoms  24884
> Precision 0.001 (nm)
> Distance between atoms 53 and 55 is 0.149, should be 0.143
> Distance between atoms 55 and 66 is 0.159, should be 0.149
> Distance between atoms 70 and 81 is 0.155, should be 0.149
> Distance between atoms 72 and 75 is 0.160, should be 0.153
> Distance between atoms 102 and 104 is 0.152, should be 0.143
> Distance between atoms 104 and 120 is 0.154, should be 0.149
> .
> .
> .
>
> then
>
> Reading frame       1 time    2.000   Distance between atoms 11 and 13 is
> 0.139, should be 0.134
> Distance between atoms 15 and 17 is 0.162, should be 0.154
> Distance between atoms 26 and 28 is 0.148, should be 0.154
> Distance between atoms 26 and 44 is 0.158, should be 0.149
> Distance between atoms 31 and 34 is 0.147, should be 0.153
> Distance between atoms 48 and 51 is 0.155, should be 0.149
> Distance between atoms 51 and 53 is 0.129, should be 0.134
> Distance between atoms 55 and 57 is 0.160, should be 0.154
> Distance between atoms 55 and 66 is 0.154, should be 0.149
> Distance between atoms 70 and 81 is 0.159, should be 0.149
> Distance between atoms 78 and 79 is 0.121, should be 0.126
> Distance between atoms 81 and 82 is 0.119, should be 0.123
> .
> .
> .
> and so on. What do you think about that?
>
> Best wishes,
> Dawid
>
> 2017-07-28 13:33 GMT+02:00 Mark Abraham <mark.j.abraham at gmail.com>:
>
> > Hi,
> >
> > It's hard to tell without seeing the messages and knowing whether those
> > bonds were constrained.
> >
> > Mark
> >
> > 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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