I check the animation of VMD again, and found that during the animation, some H-H connections are displayed. But as the time grow, they disappear sooner or later. On the other hand, the mdrun didn't crash for 500 ps ( 0.001ps/step). Therefore, I think it is the problem of the display of VMD.
I used the g_mindist to calculate the minimal distance of all the hydrogens (Firstly I select all the hydrogens as one group in make_ndx, then use only this group in g_mindist ), found that generally it is bigger than 0.12nm, but there is one strange point, it is about 0.1 nm (0.0995nm).
Therefore, 1) it is true that there are some short H-H distances during the MD, 2) the mdrun is ok.
I think I can trust the result of mdrun, but I need a longer mdrun.
Thanks for all!!
2006/10/24, Mark Abraham <[EMAIL PROTECTED]>:
Well the URL I provided above omits PDB files from the list of file
types that VMD reads for bond connectivity. Hence I suspect Baofu has
misinterpreted something, or that manual section is incomplete.
Mark
--
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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