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

Qiao Baofu qiaobf at gmail.com
Mon Oct 23 17:27:22 CEST 2006

Thanks.  Now I understand what happens.

But in the user-manual of VMD, it is said that only four Gromacs file (GRO,
G96, XTC, TRR) and .pdb can be read by VMD. But only the .pdb contain the
information of bond-connectivity (if I understand correctly). The point is
that the output .pdb file from mdrun contains only the coordinate
information!  How can I tell VMD the bond-connectivity information?!!

I used the "mol new myfile.gro autobonds 0" to see my molecules.
Unfortunately, only atoms are displayed, no connection.

2006/10/23, Ignacio Fernández Galván <jellby at yahoo.com>:
> --- Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
> > Right, so like I said earlier, you're not giving it your topology,
> > because you're loading from a .gro file. Instead, VMD is making stuff
> > up
> Incidentally, you can disable this behaviour by loading the file in VMD
> with "mol new myfile.gro autobonds 0" (or something like that).
> Send instant messages to your online friends http://uk.messenger.yahoo.com
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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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