[gmx-users] Non bonded interaction mapping

Dan Gil dan.gil9973 at gmail.com
Fri Aug 11 16:39:57 CEST 2017

Hi Sameer,

There is a quick and easy way to visualize hydrogen bonds. Convert your
traj.trr file to .gro and open it in VMD software. You can then manipulate
VMD options to show hydrogen bonds.


On Sun, Aug 6, 2017 at 10:57 AM, Sameer Edirisinghe <nootsam at gmail.com>

> Dear all,
> I have done 200ns simulation for my polymeric system and I want to map all
> existing nonbonded interactions (i.e. H bonds) in my system over the time.
> Can anyone suggest me a method for this?
> Regards
> Bhagya karunarathna
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