VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Tue Jul 24 2012 - 06:22:00 CDT

On Tue, Jul 24, 2012 at 11:53 AM, Nidhi Jatana
<nidhijatana_at_bic-svc.ac.in> wrote:
> Dear Sir/Madam
> This is Nidhi Jatana, working as Senior Research Fellow,
> Bioinformatics Center, Sri Venkateswara College, University of Delhi.
> I am running simulations on a membrane protein using Desmond and I
> want to convert the trajectories and energy file (.ene file) to those
> compatible with Gromacs. How can I do it using VMD?

don't the recent gromacs tools allow to use VMD molfile plugins?
that would take care of the trajectory files. with energy data you
are out in the cold, since VMD (or molfile) doesn't handle that.

> And also, I want to know is there any way to calculate area/lipid in
> VMD for the entire trajectory?

have you searched the mailing list archives? this is a
topic showing up repeatedly, and perhaps somebody
posted some instructions at some point.

axel.

>
> Thanking you
>
> Regards
>
> --
> Nidhi Jatana
> Senior Research Fellow
> Bioinformatics Center
> Sri Venkateswara College
> (University of Delhi)
> Dhaula Kuan
> New Delhi-110021.
> 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
International Centre for Theoretical Physics, Trieste. Italy.