My hunch is that for many simulations at 300K TIP3P with current
force-fields is better than TIP4P-Ew. Small molecule solvation is a
documented example. On the other hand, TIP3P does not get the structure of
water right, TIP4P-Ew does a better job.
For #1, I suspect that TIP3P is still better if the goal is to simulate the
native state, as TIP3P seems to over stabilize it. In addition,TIP3P's
self-diffusion is too times higher than that of TIP4P-Ew (and experimental
value), which may slightly speedup the conformational sampling..
#2: 373K is dicey, as TIP3P temperature dependence is bad. On the other
hand, others have used TIP3P at high temp. as well. I am not sure if
TIP4P-Ew is better.
#3. Newer 4-site waters may be worth the extra expense, but probably not
TIP4P-Ew.
#4. At the moment "No.". Not for biological simulations.
Also, in cases where electrostatic interactions are important (e.g. RNA/DNA
simulations), models with more accurate electrostatics perform better. Note
that the extra point charges do not always guarantee better electrostatics
for the model: TIP4PEw represents the electrostatics of water better than
TIP3P, but TIP5P is less accurate in that respect. More recent 3-site
models can be more accurate than older 4-site models (TIP4P); newer 4-site
models are probably most accurate in terms of electrostatics.
Hope that helps..
best,
Saeed
On Tue, Jan 17, 2017 at 7:21 AM, DmitryASuplatov <genesup.gmail.com> wrote:
> Dear Amber users,
>
> I am using TIP4P-Ew water model for a "general-purpose" protein-in-water
> simulations at 300K with PME electrostatics and FF14SB field.
>
> Please provide your best guess to the following questions:
>
> 1/ Is this (TIP4P-Ew) a good choice of a water model?
>
> 2/ Would it still be a good choice of a water model if I want to
> simulate at 373K?
>
> 3/ Would you say that 4-site water is better than 3-site water (e.g.,
> TIP3P) and worth the extra computing power?
>
> 4/ Would you say that upgrading to the 5-site water would do a better
> job (~ provide more meaningful biological predictions of a protein
> behaviour in a water solution)?
>
> Thank you.
>
> Dmitry
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Received on Tue Jan 17 2017 - 21:30:03 PST
