On Tue, Apr 16, 2013 at 1:57 PM, Jonathan Gough
<jonathan.d.gough.gmail.com>wrote:
> Hi All,
>
> I'm running some basic peptide (~15 residues)- protein (~90 residues)
> binding simulations for a friend/colleague. I just want to make sure I'm
> dotting all my i's and crossing all the t's in case he tries to publish
> this down the line.
>
> Presently I have been using the TIP3P solvent model in combination with
> running MM-PBSA. Are we going to run into (should we be concerned) any
> issues (reviewers-artifacts-etc.)? Would it be safer/smarter to use TIP4P
> or TIP5P?
>
To add to Brian's answer, if you are looking at phenomena that depends
measurably on the water model, then you should pick the 'right' one (look
in the recent literature for this). For most applications, especially
protein applications, I've never had a problem with TIP3P (I always use
TIP4Pew for RNA/DNA calculations, as I work with Brian's group on those
simulations ;).
Given how widely-used TIP3P is, and how water is stripped and treated
implicitly in MM/PBSA simulations, anyway, I don't think you have anything
to worry about using TIP3P here (sticking my neck out a bit here).
That said, the suggested articles do make for informative reading. (FWIW,
TIP3P simulations will parallelize with pmemd.cuda.MPI whereas TIP4Pew
simulations will not due to the presence of extra points, if that impacts
your decision at all).
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Tue Apr 16 2013 - 13:00:03 PDT
