[gmx-users] The Cut-off for coulombtype heat up the water system?

Mark Abraham Mark.Abraham at anu.edu.au
Sat Jun 20 03:54:46 CEST 2009

Florian Dommert wrote:
> * Mark Abraham <Mark.Abraham at 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.


More information about the gromacs.org_gmx-users mailing list