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

Qiao Baofu qiaobf at gmail.com
Mon Oct 23 14:18:43 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.

PS: I have succeeded in simulating a samller system by using the same
force-field. So I think the .itp file should be right.

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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