Re: PME and infinite polymer

From: Axel Kohlmeyer (
Date: Fri Jul 25 2008 - 08:24:30 CDT

On Thu, 24 Jul 2008, Arturas Ziemys wrote:

AZ> Hi,

AZ> I have general question. I created "infinite" polymer using binds
AZ> across boundaries. I that kind of advice be Peter here in mailing
AZ> list for nanotube, or Cruz-Chu paper of silica did that using NAMD.

AZ> Q. How well PME is compatible with such a system ?


that depends a lot on what your polymer depends of, if and how
your are solvating it, what kind of properties you want to
compute and what level accuracy you expect.

when using PME or any equivalent periodic solver for electrostatics
you are imposing an "infinite crystal" setup onto your system.
this is found to be the best compromise between accuracy and
system size for computing long range electrostatic interactions
in bulk liquid water. now if you put something into your water
box, that will be interacting with its periodic images in a
3d crystal-like fashion as well, which infers some artefacts,
if your system has a significant dipole or higher residual
multipole moments. to use such a 3d-ewald sum on a 2d-system
people frequently enlarge the non-periodic dimension in the
hope to minimize the coupling between the periodic images,
similar for 1d-systems. without going too much into technical
details (i wrote half a thesis about this and it can get pretty
nasty) one has to understand that this does not help much if
you have a resident multipole (particularly a dipole) along
the "non-periodic" dimension, e.g. in a lipid bilayer. you
will still have artificial changes (sometimes significant)
of the electrostatic potential along that directions and
even with a "proper" 2d-ewald summation, you may see some
artefacts when using spherical cutoffs.

that being said, if you add up the errors of using a force
field, statistics and other simulation "tricks" (e.g.
multi-timestepping) and you are not after sensitive properties
or trying to compute ultra-accurate numbers, it may work
just fine.

to give a comparative example, in typical peptide simulations
these days, the amount of solvating water between the periodic
images of the peptides is predominantly chose quite a bit
on the small side for the sake of computational efficiency
and i sometimes wonder if people are aware how much their
trajectories are affected by this. yet a lot of useful things
can be still be learned from those runs and i suspect that
generally the statistical errors outweigh the systematic ones,
with the exception of a few pathological cases.

so it all boils down to understanding the side effects
of using PME and checking carefully how much your system
would be affected.

hope that helps,

AZ> Arturas

Axel Kohlmeyer
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
If you make something idiot-proof, the universe creates a better idiot.

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