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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