Re: AMBER: How to reimage the trajectories of LES calculations?

From: Carlos Simmerling <>
Date: Wed, 21 Mar 2007 13:04:03 -0400

if you are calcualting diffusion behavior you imght not want to image.

ptraj might work- it may be that all of the copies are in the same residue,
Tom Cheatham would know if ptraj can image by atom or only by residue.

On 3/21/07, Kailee <> wrote:
> Dear all,
> I have done a 1ns md simulation (seperated into 10 calculations) of hydrogen
> molecule diffusion into a big protein using LES method. And I have made 1000
> LES copies of the hydrogen molecule. Now I want to analyse the trajectory
> files. When I load the trajectories into VMD, I found that there are many
> hydrogen molecules flied out of the primary box, can I ask how can I reimage
> them back to the central box? what is the difference in doing so between the
> simulations with and without LES method?
> Thanks very much for any suggestions.
> Best regards,
> Kailee

Carlos L. Simmerling, Ph.D.
Associate Professor                 Phone: (631) 632-1336
Center for Structural Biology   Fax:   (631) 632-1555
CMM Bldg, Room G80
Stony Brook University        E-mail:
Stony Brook, NY 11794-5115
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Received on Sun Mar 25 2007 - 06:07:13 PDT
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