Florian Dommert wrote:
* 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 ?
I'm going to presume you mean "a non-neutral charge" instead of "any
kind of partial charges". Certainly Xavier's right, in that I've never
seen an Ewald derivation that didn't start by assuming electric
neutrality. Such a system would have an infinite potential, of course.
The issue's been discussed on this list several times, and I don't
recall any startling outcomes. Fortunately, there are likely to be very
few biological systems where such neutrality is awkward to contrive.
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.
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.
Mark
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