Dear Saeed,
thank you for the detailed comments.
My specific situation is that I want to simulate conformational
rearrangements in protein structures (e.g. movement of loops) in water
at 300K on a microsecond scale (500 - 1000 ns) using classical MD. I
expect that some conformational rearrangements should happen but do not
want to accelerate them by increasing the temperature, so instead I
calculate longer trajectories.
From your reply I conclude that TIP3P "... may slightly speedup the
conformational sampling ..." - so this is exactly what I need, right?
However in the previous sentence you say that "...TIP3P seems to over
stabilize...the native state" which seems to contradict with the first
statement...
I am also confused about your overall negative attitude towards the
4-site waters. My naive expectation was that 4-site models should
generally be always better that 3-site models and thus worth the
processing overhead. Otherwise, why would anybody use them, right?
If TIP4P-Ew model is so bad than why was it used in [Shaw D. E. et.al.
Science 2010 , 330, 341] and also in this Amber tutorial -
http://ambermd.org/tutorials/advanced/tutorial22/ ???
Finally, is there some general guideline on how-to choose a water model
for a particular task.
Thank you for your time.
Dmitry
On 01/18/2017 08:13 AM, Saeed Izadi wrote:
> 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
> <mailto: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 Wed Jan 18 2017 - 03:30:03 PST
