AMBER Archive (2005)

Subject: AMBER: How to set the virtual box size for a calculation run in vacuum

From: Li Su (suli_at_msu.edu)
Date: Mon Jun 20 2005 - 08:27:33 CDT

Dear Amber Users,
 For I'm running alanine dipeptide in vacuum using Langevin Dynamics, it
always goes out of the virtual box. I'm wondering if there is a way to set
the size of the virtual box to be much larger. And by the way, whether there
is a way for amber to analyze the trajectory to get the center of mass
trajectory? Thank you in advance!

 

Best Wishes,
Li

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