AMBER Archive (2007)

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

From: Kailee (kaileeamber_at_googlemail.com)
Date: Wed Mar 21 2007 - 07:35:06 CST

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

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