Re: Rise in Total Energy in NVE

From: Chris Harrison (char_at_ks.uiuc.edu)
Date: Wed Jul 09 2008 - 20:46:53 CDT

Sourav,
1 fs should be adequate. If significant drift continues to occur, you
might attempt 0.5fs to see if it decreases drift, but 1fs should be
sufficient.

-Chris

On Wed, Jul 9, 2008 at 12:33 PM, S.K. Ghosh <skg30_at_cam.ac.uk> wrote:
> Peter,
>
> Thanks for your suggestion. Is 1 fs OK to work with non-rigidbonds? or would
> 0.5 fs be more appropriate?
>
> Thanks,
> Sourav
>
> On Jul 9 2008, Peter Freddolino wrote:
>
>> Hi Sourav,
>> 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.
>>
>> Peter
>>
>> 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.
>>>
>>> Thanks,
>>> Sourav
>>>
>>>
>>> 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.
>>>> Peter
>>>>
>>>> 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.
>>>>>
>>>>> Thanks,
>>>>> Sourav
>>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>
>
>

-- 
Chris Harrison, Ph.D.
Theoretical and Computational Biophysics Group
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801
char_at_ks.uiuc.edu Voice: 217-244-1733
http://www.ks.uiuc.edu/~char Fax: 217-244-6078

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