* Mark Abraham <mark.abra...@anu.edu.au> [2009-06-19 14:55:02 +1000]:
Chih-Ying Lin wrote:Hi People conclude that the heating up is normal by using a plain cut-off. So, how to fix the problem?0. Do more background reading. :-)1. From Berk => use multiple groups. => how ??? => I have been thinking that it is better to group the molecule => such as: protein , non-protein 2. change the coulombtype without the coulomb cut-off rcoulomb ? => such as PME, PPPM ? => what's the suggestion about this? 3. Normally, how do people fix this problem?These days, PME will tend to be the easiest to defend in a publication. You will have lower heating problems with various modified forms of cut-offs and/or longer cut-offs, but then you have the problem of justifying the use of the force field, which was probably parametrized for some other coulomb scheme.
Hi Mark, Can you please explain me or provide am reference explain why I am not able to use a SPME/PME/PPPM/EwaldSum method for any kind of partial charges living in an environment with periodic boundary conditions ? 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 inaccurateelectrostatic 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 ? However I am always open to enhance my experience and knowledge therefore please let me know if understood anything wrong. Flo
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