[gmx-users] strange new H-H bond formation during MD
Mark.Abraham at anu.edu.au
Mon Oct 23 20:59:09 CEST 2006
Qiao Baofu wrote:
> 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?!!
PDB files do not contain bond connectivity. By the look of
http://www.ks.uiuc.edu/Research/vmd/current/ug/node21.html, you can't
tell VMD your gromacs connectivity, unless you write your own plug-in to
VMD (hint, hint). You could also try asking the VMD mailing list. Your
simplest plan is likely to be to generate a PSF or PARM file with an
equivalent topology, for they are used in other MD codes to contain the
VMD is showing these bonds because the H atoms are getting close enough
to qualify as bonded by its rules. As I suggested in my first reply, are
you sure that this proximity doesn't mean your simulation is broken
somehow? If so, that would also solve your problem - just not so usefully!
> I used the "mol new myfile.gro autobonds 0" to see my molecules.
> Unfortunately, only atoms are displayed, no connection.
Well, that's what that command asks it to do :-)
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