Florian Dommert wrote:
* Mark Abraham <mark.abra...@anu.edu.au> [2009-06-20 11:54:46 +1000]:
When I understood the idea of the reaction field correctly, I treat the
electrostatic forces with a cutoff and relative dielectric permittivity
!= 1. With the mentionend Ewald methods I should be able to reproduce
exactly the same circumstances like in a reaction-field setup. So at the
moment I can imagine just one critical point, when using SPME/PME/PPPM
or an Ewald sum is the big set of parameters that have to adapted in
order to obtain an appropriate accuracy of the forces. In the reaction
field method you just have two parameters: the cutoff and epsilon_r. The
other algorithms require addtionally require the input of an appropriate
size for used grid in Fourier space and in case of SPME/PME/PPPM also an
interpolation order. Finally you need to set the splitting paramter
correctly, otherwise you will obtain unaccurate forces. So there can be
a very large error introduced, when applying the wrong parameters to the
Ewald methods. The heat up of the water is also just related to
extremly inaccurate
electrostatic forces, since with PBC an "infinite" system is
simulated and just a very small amount of the electrostatic
interaction that is of
long range nature is calculated. Therefore an large error is not
unexpected.
Finally the only restriction of Ewald I see is the requirement of PBC,
where I can reach any level of accuracy for the electrostatic force
given by certain charge distribution, don't I ?
I really haven't understood you, sorry.
I think that I a complete wrong idea of an simulation using a Reaction
field, so I have to get a correct picture. Because when investigating a
protein you require a physiological environment with corresponding ions
to provide a certain pH value. Is this finally all contained in the
force field parameters ?
In principle, yes, however not even in theory is this true for the
commonly-used force fields. Typically they were parameterized to
reproduce a range of experimental or quantum-chemical data, but the
scale of this parameterization problem was large enough that considering
solvents of non-pure water would have been too much (even if data was
available). One might demonstrate post-factum that a force field does a
reasonable job in such a case. One might also demonstrate that a force
field does a reasonable job under a different electrostatic treatment.
This would make things clear and enlight my
foggy insight in this special way to treat electrostatic forces.
Furthermore I assume no periodic boundary conditions are used then ?
One's electrostatic model need not be confounded with the boundary
conditions of the simulation. For Ewald-family methods, PBC is required,
introducing the potential for periodicity artefacts. For other methods
(cut-off, fast multipole and variants) one has the option of choosing a
different boundary condition (e.g. non-periodic (RF) vacuum containing a
restrained spherical shell of water around free water, or a large
protein complex in vacuo) and suffering artefects from those boundary
conditions, rather than perhaps periodicity-induced ones.
In particular for RF, the assumption of homogeneity would suggest not
using PBC. With enough solvent, in practice that assumption would be
approximately true even under PBC.
You just simulate a protein/polymer/molecule and assume that it is
surrounded by a medium with a certain epsilon_r.
Sure, but the RF model as applied to each particle does not depend
strongly on whether the system is periodic if the system has enough
solvent per image.
Mark
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