[gmx-users] The Cut-off for coulombtype heat up the water system?
dommert at icp.uni-stuttgart.de
Sat Jun 20 16:18:20 CEST 2009
Thanks for the detailed reply. This is a really good example for the
manifold of traps you can tap into when treating long range forces.
* Mark Abraham <Mark.Abraham at anu.edu.au> [2009-06-20 14:55:39 +1000]:
> Florian Dommert wrote:
>> * Mark Abraham <Mark.Abraham at 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
>>>> 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.
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