VMD defines the bonds according to a distance criteria.
Note that these are not defined in a gro or trr file but in the tpr,
which
is not red by VMD.
If your distances are not seen this means that the atoms are not within
the VMD's criteria. Are you using a CG model where the distances
are larger than the usual atomistic ones?
One solution is to use a dynamic representation in VMD where you
can set the atoms link by a bond based on a cutoff.
XAvier.
On Feb 19, 2009, at 8:59 AM, He, Yang wrote:
Hi all users,
When I try to input the .gro and .trr file into the VMD, I always
find that there is no bond connected among the atoms.But in fact, I
have defined all the bond connection in the gromacs files. Can
anyone tell me how to get the snap shots in the VMD with the bonds
among the atoms?
Thank you in advance.
Yang
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