AMBER Archive (2003)

Subject: Re: AMBER: high temperature, 498K, unfolding simulations

From: Andreas Svrcek-Seiler (svrci_at_tbi.univie.ac.at)
Date: Thu Nov 13 2003 - 11:05:46 CST


Hi,
> I have noticed in a recent paper (PNAS vol 100, p13287) from Daggett's and
> Fersht's groups that they have been using a 2fs time step at 498K
> (although they weren't using AMBER). I am wondering if such a long time
> step is a good idea at this temperature and am currently running
> simulations with 1fs time steps and 2fs time steps at 500K to see what
> differences there are.
I'd say that as long as it's numerically stable, it's ok. MD at 498 K
is a way to untangle a structure but not to obtain the actual behavior
of the respective molecule at that temperature (does anyone know
the boiling temperature of TIP3P water ?) - That's only my personal
opinion. Others (with more experience) might have a different opinion.

Best regards
Andreas

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