Re: namdenergy strange behaviour !!!

From: Brian Bennion (
Date: Mon Sep 17 2007 - 11:15:18 CDT

It may be that the energy being reported is the average energy and at
the first time step of a restart the average wiil be missing previous

This behaviour is always seen when using the following command

namdplot PRESSAVG vs TS logfile.log

May be it is the same for the namdenergy plugin?


At 07:49 AM 9/17/2007, paco ty wrote:
>Hi list,
>runing namdenergy from VMD 1.8.5 to calculate the
>interaction energy between protein and solvent, I
>realized, that for each succesive run of a simulation
>the energy drops from about -200 to about -1000, while
>expecting rather a continuation (the starting energy of
>some run to be the last of the previous). The namd energy
>log file looks quite normal with all energy contributions
>remain "constant".
>The dcds come from NVT equilibrations with namd 2.6,
>spherical BC and "langevin on".
>Namdenergy is a very usefull tool and it would be a pity
>if there is some snare under some conditions and the
>results were useless.
>Does anybody understand this behaviour?
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