[gmx-users] The Cut-off for coulombtype heat up the water system?
dommert at icp.uni-stuttgart.de
Sat Jun 20 05:14:30 CEST 2009
* 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
>> 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 ? 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 ?
You just simulate a protein/polymer/molecule and assume that it is
surrounded by a medium with a certain epsilon_r.
>> However I am always open to enhance my experience and knowledge
>> therefore please let me know if understood anything wrong.
> Indeed - I've always found that a key attribute in a research scientist.
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