On Mon, Nov 21, 2011, Bruno Rodrigues wrote:
>
> It has been suggested here by the specialists (I guess David Case) that for
> TIP4P and TIP5P water ffs the time step for solvated biomolecules should be
> decreased.
>
> I have observed that high temperature DNA simulations are not stable at 2fs
> for these two ffs, obligating me to go down to 1.5 and 1.0fs respectively.
It's hard to say much here. We don't know what temperature you are using,
what DNA force field, or what the definition of "not stable" is.
I might make two general comments. First, DNA is kind of on the "edge" of
stability with current force fields, and once some strands start to unravel,
that process can continue. I'd guess that using high temperatures would
exacerbate this.
Second, 2fs time steps are also pushing things. They almost always require
thermostatting to keep the temperature from drifting, and the extra energy
is often very localized (arising from a badly-integrated atomic collision),
which can sometimes disrupt local structure in a way that is not re-annealed.
I generally use 1fs steps, but sometimes don't. Clearly, if you are seeing
problems at 2fs that seem to go away at 1fs, you should probably be using
the short time step.
....dac
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Received on Mon Nov 21 2011 - 09:30:03 PST
