All very helpful! Thank you!
Papers have been downloaded and in my queue for reading =)
Jonathan
On Tue, Apr 16, 2013 at 3:31 PM, Jason Swails <jason.swails.gmail.com>wrote:
> 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 - 13:00:04 PDT
