From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Wed Jul 09 2008 - 10:37:19 CDT
spherical boundary conditions do work on the system (since they're
applying forces). A rise in energy should not be surprising.
Also, you may need to avoid multiple time stepping (ie, change
fullElectFrequency to 1) to get perfect energy conservation.
S.K. Ghosh wrote:
> Hi Peter,
> I am now sending this to the group.
> Hi All,
> 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 0.5 fs?
> Or is this because of the following multistepping that I am using.
> timestep 1
> #rigidBonds all
> nonbondedFreq 1
> fullElectFrequency 2 stepspercycle 10
> 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 decreased.
> In both the runs, I have used spherical boundary conditions.
> Your comments would be much appreciated.
> On Jul 7 2008, Peter Freddolino wrote:
>> Hi Sourav,
>> 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 this.
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:48:02 CST