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

Mark Abraham Mark.Abraham at anu.edu.au
Tue Apr 28 04:00:32 CEST 2009

He, Yang wrote:
> Hi all users,
> I want to get some snap shots from VMD through inputing my gro and trr file to  the VMD. But I always find that I can not get the bond connection among the atoms and then, I try to use the dynamic bonds to solve this problem but  another problem is that  when I define a value for the cutoff distance, the bonds which don't exist among the atoms in the original shape will also come up .

VMD guess at bonds based on atom names and inter-atomic distances, so 
your .gro file isn't following the rules it expects. Either your 
structures are broken, or they're coarse-grained and you need to tell 
VMD to use suitable rules, or something similar.


> Except the dynamic method to figure out this problem, I wonder whether there are other ways to fix this problem.
> Thank you for any suggestions.
> Yang
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