[gmx-users] Why density increase with increasing the cutoff length?
Mark.Abraham at anu.edu.au
Mon Dec 21 11:01:17 CET 2009
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.
> But I think we all agree on these issues: the treatment of long-range
> interactions are delicate :))
Agreed, treating long-range interactions is delicate :-)
> On Sun, Dec 20, 2009 at 11:03 PM, Yanmei Song <ysong30 at asu.edu
> <mailto:ysong30 at 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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