[gmx-users] neutral plasma

[Mark Abraham]

On 8/12/2010 4:52 AM, Igor Marques wrote:
> Hello everybody,
>
> I've digging around the user manual, the website and the mailing list 
> archives and I'm afraid I might be missing something: does GROMACS 
> have some kind of /neutral plasma /as AMBER does?

You're probably referring to some descriptions of the technique 
underlying the Ewald method.

> Or every simulation must have a net charge of 0.000 ?

All the Ewald derivations I have seen require neutrality of the 
simulation cell, however that requirement can finessed by introducing a 
neutralizing plasma for each charged entity. I learned about this issue 
a while ago in a namd-l thread 
http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/3976.html. The 
reference Hyonseok cites (T. Darden, D. Pearlman, L. G. Pedersen, JCP 
v109, p10921, 1998) covers the issue well, and the salient point for MD 
in GROMACS is that the self potential in (2.16) vanishes under the 
differentiation that forms the forces from the energy. So the forces are 
right regardless. That reference does post-date the SPME paper that 
GROMACS implements. I'm not sure if GROMACS has the correct self-energy 
for non-neutral cells, but that only affects the total energy as an 
additive constant.

Perhaps Berk or Carsten can enlighten us about the self-energy 
implementation.

Mark
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