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
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