[gmx-users] gmx check

[Dawid das]

Thank you for explaining.

Best wishes,
Dawid

2017-07-28 15:11 GMT+02:00 Mark Abraham <mark.j.abraham at gmail.com>:

> 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
> > > > --
> > > > Gromacs Users mailing list
> > > >
> > > > * Please search the archive at
> > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > > posting!
> > > >
> > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > > >
> > > > * For (un)subscribe requests visit
> > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> or
> > > > send a mail to gmx-users-request at gromacs.org.
> > > >
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at http://www.gromacs.org/
> > > Support/Mailing_Lists/GMX-Users_List before posting!
> > >
> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >
> > > * For (un)subscribe requests visit
> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > > send a mail to gmx-users-request at gromacs.org.
> > >
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>