[gmx-users] strange new H-H bond formation during MD

Mark Abraham mark.abraham at anu.edu.au
Mon Oct 23 15:03:21 CEST 2006

> Hi All,
> I meet a problem in run MD: from the display of VMD, there are some H-H
> bonds formed during the MD. All the bonds I wrote in .itp file are right,
> except these new unexpected H-H bonds.  (I generate the system from a
> smaller system, EM is ok,  when running NTV, the problem comes. )  Who can
> give some suggestions? Thanks in advances.

Unless you opened the structure from a .tpr file, VMD can't even have
accessed your topology. It has its own heuristics for deciding whether to
show a bond exists. See the VMD documentation for details. Whether these
close H-H contacts are a problem is for you to judge :-)


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