AMBER Archive (2007)

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

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Wed Mar 21 2007 - 11:04:03 CST

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 <kaileeamber_at_googlemail.com> 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: carlos.simmerling_at_gmail.com
Stony Brook, NY 11794-5115
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