The Temperature is quite high: 400K, and I'm using parmbsc0 on Amber11 for
a 10bp short sequence.
However my question is: what makes TIP4P and TIP5P less stable than TIP3P???
Because I achieved a very nice result on the denaturation process using
TIP3P with 2fs, but with both other force fields the energy started to
drift until gets higher and higher values and the system became unstable,
interacting with the 1st image, and so on.... Then I switch to 1fs and it
nicely melted as expected.
I've read your paper (J. Phys. Chem. B 2008, 112, 6013-6024) and followed
your instructions there about the water force fields. Do you think that
there might exist some kind of internal vibration on DNA that is very
sensitive to Coulomb forces? I have accurately calculated the water
self-diffusion for the TIP5P up to 400K, in long NVE simulations after NpT
equilibration and found that for TIP5P it has a higher value than for both
TIP3P and TIP4P. Can it be related with the stability of the system?
I guess these are questions that still deserve much attention and research
on this field, and the answers might not exist yet.
Thank you in advance.
On Mon, Nov 21, 2011 at 3:04 PM, David A Case <case.biomaps.rutgers.edu>wrote:
> 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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>
--
--
Bruno Barbosa Rodrigues
PhD Student - Physics Department
Universidade Federal de Minas Gerais - UFMG
Belo Horizonte - Brazil
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Received on Mon Nov 21 2011 - 10:00:02 PST
