Re: Electrostatics cutoff with PME

From: L. Michel Espinoza-Fonseca (mef_at_ddt.biochem.umn.edu)
Date: Tue Apr 15 2008 - 14:00:03 CDT

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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