Arden Perkins wrote:
From what my Professor told me it is my understanding that cutoff
length is somewhat a trade-off between accuracy of the simulation and
length of time to generate the simulation. A higher cut-off indicates
more accuracy but will take longer to simulate. I use low cut-offs for
less important simulations like energy minimizations.
A higher cut-off does not necessarily indicate higher accuracy, for the
parameterization process used a particular cut-off. The model physics is
defined by all of the functional form, parameters, cut-offs, etc. The
validity of the parameters is intrinsically linked to that cut-off. One
might be able to demonstrate that one can get equivalently valid results
with a different (i.e. longer) cut-off, but then there's not yet a
demonstrated *increase* in accuracy. If the same parameters can produce
a better model physics at a longer cut-off, then there's probably a case
for further parameterization to do equivalently well for lower cost.
All this assumes a non-Ewald method. PME is a different matter entirely.
An increase in density would mean a larger number of simulated molecules
and therefore a need for a higher cut-off for more accurate data. That
is my best theory anyway.
A higher density for a given cut-off increases the number of interaction
partners for each atom, but that implies nothing about the accuracy of
the model of that system at that density. A move from one density to
another during equilibration at a given cut-off tends to indicate the
unsuitability of the model physics at the former density.
Xavier Periole:
> But I think we all agree on these issues: the treatment of long-range
> interactions are delicate :))
Agreed, treating long-range interactions is delicate :-)
Mark
On Sun, Dec 20, 2009 at 11:03 PM, Yanmei Song <yson...@asu.edu
<mailto:yson...@asu.edu>> wrote:
Dear Users:
Anyone can explain why the density of the water models increase with
increase the cutoff length. I tried a couple water models in
reaction-field, PME simulations.The cutoff length ranged from 0.9 to
1.5. They all show the same trend. Then there must be some reasons.
Anyone can tell me why?
--
Yanmei Song
Ph.D. Candidate
Department of Chemical Engineering
Arizona State University
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