From: S.K. Ghosh (skg30_at_cam.ac.uk)
Date: Wed Jul 09 2008 - 10:25:35 CDT
I am now sending this to the group.
I find the total energy rising in an NVE run:
First I ran an NVT (1 fs timestep and rigidbonds off) and then an NVE
(again 1 fs timestep and rigidbonds off) starting from where the NVT run
ended. For this NVE run, I find that the Total Energy is slightly
increasing initially (steady rise but approx 30 kcal/mol in total) for 1 ns
and looks to be almost flat for the last 1 ns (please find attached). The
temperature, however, does not rise at all.
I am curious to find out why the energy rises. Could someone comment on
that please. Is 1 fs timestep high with rigidbonds turned off? Should I use
Or is this because of the following multistepping that I am using.
I have attached the energy values for 1st and last timestep here. I can see
that DIHED, IMPRP and ELECT have increased and VDW and BOUNDARY have
In both the runs, I have used spherical boundary conditions.
Your comments would be much appreciated.
On Jul 7 2008, Peter Freddolino wrote:
>this kind of question is really better addressed to namd-l, so that
>other users can learn from your question (and search for it later).
>For this increase in total energy, what other simulation parameters
>(timestep, etc) are you using? Is the energy rise continuous or does it
>fluctuate? If you use 1 fs timesteps without multiple timestepping, you
>should conserve energy quite well over time.
>S.K. Ghosh wrote:
>> Hi Peter,
>> Starting from where an NVT ended, I ran an NVE i.e. turned off the
>> constant temperature control (the pressure control was turned off for
>> both). I found that the temperature was pretty stable but the Total
>> Energy curve showed slight increase (around 30 kcal/mol). There was no
>> change in timestep or rigidbonds or any other parameters between the
>> two runs. Though the energy rise is comparatively quite low, is this
>> something normal? I would be interested to know why the Total Energy
>> rises even though I am running an NVE run. Could you please comment on
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