Re: namdenergy strange behaviour !!!

From: Peter Freddolino (
Date: Mon Sep 17 2007 - 11:23:04 CDT

this certainly sounds odd, and I haven't seen anything like what you're
describing in the past. The usual checklist of things that might lead
to problems with namdenergy is:
-make sure you're using appropriate periodic boundary conditions,
cutoffs, and such for your simulations
-make sure you try with the latest version of vmd (1.8.6)

Also, how exactly are you loading the trajectories? Loading a psf, and
then the dcd file for each trajectory into separate molecules?


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?
> Bye
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