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

Qiao Baofu qiaobf at gmail.com
Thu Oct 26 11:15:29 CEST 2006


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 <Mark.Abraham at anu.edu.au>:
> 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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20061026/9825633b/attachment.html>

More information about the gromacs.org_gmx-users mailing list