VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Mon Jan 26 2015 - 20:50:46 CST

On Mon, Jan 26, 2015 at 7:59 PM, Bharat Sharma
<bharatsolbridge_at_gmail.com> wrote:
> Hello Experts,
> I am interested to calculate the hydrogen bond by calling "measure hbonds"
> function. I have a periodic calculation. I checked the hbonds code but did
> not able to see the line where period images are taken care.
>
> Does VMD cares hydrogen bonds formed with period images?

no.

> If not, how do I
> call it and use it?

you cannot. you'd have to use a tool that does or you'd have to work
around it, e.g. by creating a trajectory with the necessary periodic
data added and then only analyzing the hbonds for atoms within the
original volume.

axel.

> Thank you. Any suggestions are appreciated.
>
> Best Regards,
> Bharat Sharma 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.