From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Mon Sep 17 2007 - 11:23:38 CDT
This shouldn't be an issue for namdenergy, as all of the quantities it
reports are single-timestep quantities, rather than averages.
Brian Bennion wrote:
> 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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