VMD-L Mailing List

From: Neha Gupta (nehaphysics17_at_gmail.com)
Date: Thu Oct 26 2017 - 09:43:29 CDT

Hi,

Thank you for the reply.

I want to view the hydrogen bonds when VMD plays through the entire
trajectory for 5 ns.

Thanks,
Neha

On Wed, Oct 11, 2017 at 1:54 PM, Ashar Malik <asharjm_at_gmail.com> wrote:

> 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
>