From: S.K. Ghosh (skg30_at_cam.ac.uk)
Date: Wed Jul 09 2008 - 12:33:37 CDT
Thanks for your suggestion. Is 1 fs OK to work with non-rigidbonds? or
would 0.5 fs be more appropriate?
On Jul 9 2008, Peter Freddolino wrote:
>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.
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