You can use the "closest" command in ptraj and then look at the resulting
trajectory. If the water exchanges, this may help you narrow it down.
Don't forget that you'll have to create a new prmtop with the same number of
water molecules as you specified in the "closest" command in order to
visualize or do further processing with ptraj.
Hope this helps,
Jason
On Mon, Oct 4, 2010 at 6:34 PM, Lekpa Duukori <duukori.gmail.com> wrote:
> Hi all,
>
> I have a trajectory where I suspect that their may be water bridges. I want
> to check if these are present and I'm wondering if people know of a way to
> extract this kind of information using ptraj or similar.
>
> Thanks.
>
> Lekpa
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Mon Oct 04 2010 - 19:00:06 PDT
