[gmx-users] strange new H-H bond formation during MD
erikm at xray.bmc.uu.se
Tue Oct 24 09:44:38 CEST 2006
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
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.
> 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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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
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