Thanks.<br><br>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. <br><br>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). <br><br>Therefore, 1) it is true that there are some short H-H distances during the MD, 2) the mdrun is ok. <br><br>I think I can trust the result of mdrun, but I need a longer mdrun.
<br><br>Thanks for all!!<br><br><br><div><span class="gmail_quote">2006/10/24, Mark Abraham <<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>>:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<br>Well the URL I provided above omits PDB files from the list of file<br>types that VMD reads for bond connectivity. Hence I suspect Baofu has<br>misinterpreted something, or that manual section is incomplete.<br><br>Mark
<br></blockquote></div><br><br>-- <br>Sincerely yours,<br>**********************************************<br>Baofu Qiao, PhD<br>Frankfurt Institute for Advanced Studies<br>Max-von-Laue-Str. 1<br>60438 Frankfurt am Main, Germany TEL:+49-69-7984-7529
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