Dear Amberusers,
It should be rather straight forward to turn off all the "extra"
integration options and simply determine whether or not the integration
is working to the correct order in Amber or at least determine what the
order of the error is in Amber. Thus defining what "true NVE" really
means for the integrator
Then one can turn on the ewald (which introduces additional errors)
and determine how ewald affects the error. Granted ewald has numerous
options that determine its accuracy so this becomes a rather extensive
study. But this is what must be done to tease out any errors in the
implementation.
Hasn't there been a systematic analysis of error in Amber with respect
to Ewald published somewhere?
Thanks,
TOm
Thomas Cheatham wrote:
>>Tom Cheatham (he can agree/disagree) had a similar problem and found that
>>by increasing the default ewald coefficient a bit he got rid of the
>>drift. It might be that for highly charged systems the discontinuity in
>>direct sum energy/forces at the cutoff [i.e. erfc(beta*r_cutoff)/r_cutoff
>>
>>> order = 4, dsum_tol = 0.00001, eedmeth = 1,
>>>
>
> As the eminent Dr. Darden mentioned, if you just decrease dsum_tol by 1
> order of magnitude, dsum_tol = 0.000001 you should avoid this drift.
> Although Professor Duan points out that errors are expected, we can run
> under appropriate conditions true NVE for long simulations such as these
> without the drift you are seeing... However, I do not think this drift
> will significantly impact your structural/dynamic results; if you re-ran
> this simulation with better energy conservation, what you will interpret
> out of your DNA simulation will very likely not change (or at least not
> change due to energy conservation; the changes you will see will be due to
> sampling a different ensemble and as you may find out, rather long
> simulations are necessary to fully "equilibrate" DNA properties).
>
> Good luck,
>
> \ Thomas E. Cheatham, III (Assistant Professor) College of Pharmacy
> | Departments of Medicinal Chemistry and of University of Utah
> | Pharmaceutics and Pharmaceutical Chemistry 30 South 2000 East, Room 201
> | & Center for High Performance Computing Salt Lake City, Utah 84112
> |
> | e-mail: tec3.utah.edu phone: (801) 587-9652 FAX: (801) 585-9119
> \ http://www.chpc.utah.edu/~cheatham Offices: BPRP295A / INSCC 418
>
>
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Received on Fri May 09 2003 - 20:53:01 PDT
