Hi,
You can post-process your trajectories using sander imin=5 to get the total
energy and potential energy for each structure in the trajectory.
In the Amber14 manual, information for using this flag in the input can be
found on page 285.
-Christina
On Mon, Mar 30, 2015 at 6:39 AM, Wang Moye <wangmoye13.mails.ucas.ac.cn>
wrote:
>
>
> Hello everyone!
>
>
> I have a REMD process using AMBER12. There are 26 replicas in my system.
> As the tutorial said, a typical use of REMD is to obtain thermodynamic
> ensembles at temperatures of interest (e.g. 300 K). So I extracted the
> data for each temperature . Now I want to get the potential energy for
> each temperatue , what should I do next ? I have 26 mdcrd trajectories and
> the process_mdout.perl can analyse the mdout files only.
> If I want to get the total energy and potential energy through mdcrd
> trajectories , which tool should I use ?
>
>
> Thank you very much!
>
>
> --
> Wang Moye
>
>
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
---------------------------------------------------------------------------------------
Christina Bergonzo, PhD
Postdoctoral Researcher
Department of Medicinal Chemistry, University of Utah
30 South 2000 East, Rm. 201
Salt Lake City, UT 84112-5820
Office: L.S. Skaggs Pharmacy Research Institute, Rm.4290
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652 / Fax: (801) 585-6208
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Received on Mon Mar 30 2015 - 07:30:13 PDT
