AMBER Archive (2003)

Subject: Re: AMBER: 1 fs timestep for GB?

From: Alexey Onufriev (onufriev_at_scripps.edu)
Date: Tue Nov 25 2003 - 15:19:04 CST

Hi.

I would add the following:

2 fs. is certainly OK if shake is used.

One has to be a bit more careful with tautp when GB is used. I would
recommend values >= 1.0 ps, especially for unusually small systems, such a
single amino-acid.

                                                                Alexey

On Tue, 25 Nov 2003, Andreas Svrcek-Seiler wrote:

> Hi,
>
> > I noticed that people tend to use 1 fs time-step for integration in GB/SA
> > simulations. I understand that the scheme implemented does not involve
> > friction with the environment and this can give rise to faster
> > motions in some degrees of freedom of the solute. I am not sure how much
> > faster bonds fluctuate in this case, but a 2 fs integration step
> > did not produce anything strange for my nucleic acid simulation:
> ...I believe a 2 fs timestep won't hurt (at least not more than in other
> simulations). The fast motions frozen
> by SHAKE or RATTLE are bound to be similar in GB/SA and
> other types of simulations.
>
> > no drift in total energy over 10 ns - although the simulation was
> > run at constant temperature (300 K) with tautp=5.0.
> ...to check whether a large timestep/finite cutoff/error in the gradient
> leads to drifts, tautp= *say* 1.e9
> (or -better- no heat bath at all) would be more appropriate.
> The thermostat masks drifts quite efficiently.
>
> Hope it helps,
> good luck
> Andreas
>
>
>
>
> )))))
> (((((
> ( O O )
> -------oOOO--(_)--OOOo-----------------------------------------------------
> o Wolfgang Andreas Svrcek-Seiler
> o (godzilla)
> svrci_at_tbi.univie.ac.at
> .oooO Tel.:01-4277-52733
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