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

[Erik Marklund]

On Tue, 2006-10-24 at 04:59 +1000, Mark Abraham wrote:
> 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.

That's not entirely true. Normally, pdb files do not contain topological
information, but they CAN do so through a CONNECT block. This is
probably why VMD claims that ".pdb contain the information of bond-
connectivity" (don't use vmd myself, just cited Bafou above). However,
to my knowledge, gromacs completely ignores CONNECT blocks in pdb
output/input, which is why you see atoms only, and no connection.

/Erik

> 
> 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
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-- 
Erik Marklund, PhD Student, Molecular Biopcysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone: +46 18 471 4537          fax: +46 18 511 755
erikm at xray.bmc.uu.se