[gmx-users] Re: Energy minimization output

Justin A. Lemkul jalemkul at vt.edu
Wed Aug 13 12:13:43 CEST 2008

alkasrivastava at iitb.ac.in wrote:

> This is upto 40 ns after that i am not getting anything like that. I don't
> know exactly what it mean and how could i get rid of such messages.I don't
> know how to deal with it.

What it means is that you had some nasty contacts between some elements of your 
system and the surrounding water.  If the messages do indeed go away during EM, 
and the potential energy levels off to a reasonable, negative value, then things 
should be fine to proceed.


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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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