Thank you for explaining. Best wishes, Dawid
2017-07-28 15:11 GMT+02:00 Mark Abraham <mark.j.abra...@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 <add...@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.abra...@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 <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? 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