Re: counting h-bond in system with vmd

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Sat Dec 18 2010 - 04:51:30 CST

dear sara,

please post questions about VMD to the vmd mailing list.

On Fri, Dec 17, 2010 at 4:10 PM, sara <sara_15_s_at_yahoo.com> wrote:
>
> Dear All
>
> I work with confined fluid I need to calculate h-bond and liftime of h-bond in system . how do it? do I need tcl for it?

there are many ways to do this, and writing tcl scripts in VMD is one option.
VMD has a "measure hbonds" command, that can be used to determine
hydrogen bonds, if your input data follows the expected conventions (mainly
naming conventions of the atoms). how to apply this for your particular
case, is impossible to say. there is not one general way. similarly
for lifetimes,
where you have the additional complication of hydrogen bonds that may
reform quickly after being broken, for which you have to make a choice
as to how to account for them (provided that you need that level of detail).

i suggest to have a look at the literature for how other people have
computed hydrogen bonds and lifetimes (n.b. there are multiple competing
opinions for what are proper criteria for a hydrogen bond) and perhaps
also search the vmd mailing list archive for discussions on the subject
and particularly how to implement this in VMD through tcl scripts. the
may also be discussions on using the python script interface, in case
that makes a difference.

of course, you can also write a custom code in your favorite programming
language to do that.

cheers,
     axel.

> Dear All
>
> I have problem in work with vmd.
>
> I work with confined fluid I need to calculate h-bond and liftime of h-bond in system . how do it? do I need tcl for it?
>
>

--
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com  http://goo.gl/1wk0
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.

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