Re: Electrostatics cutoff with PME

From: Christopher Gillespie (gillescche_at_gmail.com)
Date: Tue Apr 15 2008 - 15:21:06 CDT

Gianluca,
I too have looked at my folded proteins with different cutoffs of 10, 12,
and 14A with no appreciable difference. Although I have heard of larger
cutoffs being detrimental.

Chris

On Tue, Apr 15, 2008 at 3:00 PM, L. Michel Espinoza-Fonseca <
mef_at_ddt.biochem.umn.edu> wrote:

> Dear Gianluca,
>
> Based on my very personal experience, the choice of a specific cutoff
> depends on the type of system you're studying and (of course) how well
> the results agree with experimental results, in case you have any.
>
> When I simulate isolated peptides (up to 60 aa), I usually use a
> relatively small cutoff value (7-8A). Surprisingly, when I tested
> large cutoff values (up to 16 A), the structure of the peptides tend
> to be over-stabilized and many times the results didn't agree at all
> with experiments. This applies specially to disordered-to-ordered
> transitions, and vice versa. So in my experience, large cutoff values
> are not good for peptide simulations. On the other hand, for
> simulations of folded proteins, I haven't seen a significant
> difference in their dynamic behavior when using cutoff values between
> 9 and 14 A. Again, that's my very personal experience with some
> specific systems. However, I assume that these observations might also
> work for other's systems.
>
> In summary, and to answer your question, I haven't observed any
> significant gain of accuracy when using large cutoff values in the
> simulation of folded proteins. However, the accuracy seems to be
> significantly affected when simulating the dynamics of peptides (i.e.,
> larger values tend to overestimate the stability of the peptide).
>
> Cheers,
> Michel
>
> On Tue, Apr 15, 2008 at 1:01 PM, Gianluca Interlandi
> <gianluca_at_u.washington.edu> wrote:
> > Dear all,
> >
> > I have a question concerning the electrostatics cutoff parameters when
> > using PME. It is common to use a cutoff of 10 A (real space calculation)
> and
> > a pairlistdist cutoff of 12 A when using PME. However, when PME is not
> used
> > the default paramenters are 12 A for the Coulomb interaction (SHIFT) and
> 14
> > A (or 13.5 A) for the pairlistdist cutoff.
> >
> > Although it is common to use a cutoff of 10 A in conjunction with PME
> I'm
> > still curious to know whether there might be any artifacts. Would it be
> more
> > accurate to use a cutoff of 12 A? Or is the gain in accuracy almost
> > negligible? Are there any comparative studies using different cutoffs
> and
> > PME?
> >
> > Thank you very much,
> >
> > Gianluca Interlandi
> >
> >
> > -----------------------------------------------------
> > Gianluca Interlandi, PhD gianluca_at_u.washington.edu
> > http://biocroma.unizh.ch/gianluca/
> >
> > Postdoc at the Department of Bioengineering
> > at the University of Washington, Seattle WA U.S.A.
> > -----------------------------------------------------
> >
> >
>
>

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