[gmx-users] Force Fields and Electrostatics

S. W. Chiu schiu at ncsa.uiuc.edu
Tue Apr 6 06:41:00 CEST 2004

We did not use a reaction field for cutoffs. 
T. Rog et al. (Acta Biochim. Polonica, 50, 789-798, 2003) conclude that
(i) cut-off simulation of neutral bilayers does not generate artefacts;
and (ii) the parameters that describe bilayer properties, deerived from
both cut-off and PME simulations are similar, although in some cases the
results of the PME simulation better reporduce the relevant experimental
On Mon, 2004-04-05 at 19:54, Ilya Chorny wrote:
> Do you include a reaction field when you use cutoffs?
> Ilya
> -----Original Message-----
> From: gmx-users-admin at gromacs.org [mailto:gmx-users-admin at gromacs.org]On
> Behalf Of Eric Jakobsson
> Sent: Monday, April 05, 2004 2:52 PM
> To: gmx-users at gromacs.org
> Cc: schiu at ncsa.uiuc.edu
> Subject: Re: [gmx-users] Force Fields and Electrostatics
> 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
> angstroms.
> 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.
> Eric
> At 08:59 PM 4/1/2004 +0000, you wrote:
> >David,
> >
> >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?
> >
> >Catch ya,
> >Dallas Warren
> >_______________________________________________
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> ---------------------------------
> Eric Jakobsson, Ph.D.
> Professor, Department of Molecular and Integrative Physiology, and of
> Biochemistry
> 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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See-Wing Chiu
4027 Beckman Institute
Univ. of Illinois
405 N. Mathews
Urbana, IL 61801

schiu at ncsa.uiuc.edu

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