VMD-L Mailing List

From: Ashar Malik (asharjm_at_gmail.com)
Date: Wed Oct 11 2017 - 03:24:28 CDT

HBond plugin: http://www.ks.uiuc.edu/Research/vmd/plugins/hbonds/

Use in script

   1. Load trajectory
   2. make selection
   3. for loop to iterate over frames
      - update selection every frame
      - Usage: hbonds -sel1 <atom selection> <option1> <option2> ... (this
      will give you hbonds between your selections in that frame)
      - delete selection
      - log it ??

This will "find" the HBonds. Is that what you meant by "visualization"? Or
do you mean you want to "literally" draw the HBonds as VMD plays through
your trajectory?

On Wed, Oct 11, 2017 at 6:04 PM, Neha Gupta <nehaphysics17_at_gmail.com> wrote:

> Hi all,
>
> How to visualize hbonds in vmd after simulations for 5 ns?
>
>
> Thanks,
> Neha
>
>
> 

-- 
Best,
/A