[gmx-users] input the gro and trr file into the VMD

XAvier Periole x.periole at rug.nl
Thu Feb 19 09:19:51 CET 2009

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,  
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.


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
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before  
> posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php

More information about the gromacs.org_gmx-users mailing list