[gmx-users] Force Fields and Electrostatics
jake at ncsa.uiuc.edu
Mon Apr 5 23:54:01 CEST 2004
We have compared cutoffs with Ewald, cutoffs of different lengths with each
other, and PME with exact Ewald. Also looked at different lengths vdw cutoffs.
The summary results that have guided us:
1. If you use cut-offs and have either ions of non-neutral charge groups
in the system, you will see definite artefacts at the cut-off distances in
the radial distribution functions. If you have a system that you can parse
completely into neutral charge groups, you will not see those artifacts.
2. If you use cut-offs in a lipid bilayer in water simulation, and you use
the computed surface dipole potential as a measure of whether the
electrostatics is good enough, you should use 20 angstrom cut-offs. There
is a significant difference between the dipole potential calculated at 15
angstrom and 20 angstrom cut-offs, but not between 20 angstroms and 25
3. Based on simulations of hexane (and analogy between hexane and the lipid
interior of membranes) we feel that one should use a 20 angstrom cut off
for vdw in membrane simulations. (I know that some people use less, but if
you do the liquid hydrocarbon calculations, the results are flaky unless
you use a cut off that long. The vdw does fall off as the 6th power,
therefore faster than the electrostatics, but there is no shielding of the
vdw---all the long range interactions are attractive, and therefore have a
cumulative effect at larger distances than one would otherwise think.)
4. The artefact to worry about for PME is that, since it is not strictly
conservative, the center of mass of the whole system may move. We never
had to use center of mass corrections until we started using PME. We know
that artefacts associated with uncorrected center of mass motion and PME
grow to dramatic size much more slowly if one updates the neighbor lists
every time step; the big problem seems to come when particles move across
the explicit/Fourier boundary and the system doesn't adjust the neighbor
list immediately. If you want to compute something really amusing,
simulate a box of water using PME, leave about 5 time steps (10 fsec)
between each neighbor list update, and use the NPE ensemble. Many sins are
coated over by coupling to a temperature bath!
I hope this is helpful. The real expert on this is See-Wing Chiu in our
group, who did all the calculations I described above.
At 08:59 PM 4/1/2004 +0000, you wrote:
>Thank you for the reply, much appreciated.
>Is there anyone else out there that had simulated the same system using
>different treatment of the electrostatics? And find a difference, or not?
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Eric Jakobsson, Ph.D.
Professor, Department of Molecular and Integrative Physiology, and of
Senior Research Scientist, National Center for Supercomputing Applications
Professor, Beckman Institute for Advanced Science and Technology
4021 Beckman Institute, mc251
University of Illinois, Urbana, IL 61801
ph. 217-244-2896 fax 217-244-2909
(Currently on leave to the National Institutes of Health in Bethesda,
Maryland, to be Director of the NIGMS Center for Bioinformatics and
Computational Biology and Chair of the NIH Biomedical Information Science
and Technology Initiative Consortium, but maintaining my research lab at
Illinois by periodic commuting. My usual schedule is four days a week at
NIH and three days a week at Illinois.)
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