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

[Mark Abraham]

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 
connectivity.

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 :-)

Mark