AMBER Archive (2006)

Subject: RE: AMBER: SHAKE, TIP3P and 2fs Timesteps

From: Andreas Svrcek-Seiler (svrci_at_tbi.univie.ac.at)
Date: Wed May 31 2006 - 13:38:29 CDT

Hi,
>
> On an aside I believe a number of people now consider 2fs with shake to
> really be on the bleeding edge of what you can safely use. This is with
> regards to energy conservation etc when running in the NVE ensemble. For
> safety you should probably use a 1.5fs timestep even with shake.
>
...Just my 0.02$: Long ago I played around with droplet dynamics.
Though that is bad (except as a toy), I observed *no* discernible
drift of total energy over 7 nanoseconds with NVE and a 2 fs timestep.
The statistics can be seen here:
http://www.tbi.univie.ac.at/~svrci/sample.ps
(-> a page from my thesis)
So if there's a drift with 2 fs, it might not come from SHAKE
(or home-brewn RATTLE, in that particular case, which should be the same).
By the way: I did a RNA tetraloop (~400 atoms) + ~1800 TIP3P waters at
300K.

good luck
Andreas

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