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 <[EMAIL PROTECTED]>:
> 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
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