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

Qiao Baofu qiaobf at gmail.com
Mon Oct 23 15:15:59 CEST 2006

Hi Mark,

Thanks for your reply.

I used these:
  1. vmd em_out.gro
  2. use the "load data into molecules...", select md1.trr, and then load
  3. when the anmination is finished, I can see some H-H bonds.

2006/10/23, Mark Abraham <mark.abraham at anu.edu.au>:
> > 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 :-)
> Mark
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Sincerely yours,
Baofu Qiao, PhD
Frankfurt Institute for Advanced Studies
Max-von-Laue-Str. 1
60438 Frankfurt am Main, Germany TEL:+49-69-7984-7529
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