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 <add...@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-requ...@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-requ...@gromacs.org.