On 30/01/11 16:13, David van der Spoel wrote:
On 2011-01-30 17.08, ms wrote:
On 30/01/11 15:41, David van der Spoel wrote:
Since I have exactly the same needs (charged system in vacuum) I jump
in...
In http://www.gromacs.org/Documentation/Errors
it says:
Note for PME users: It is possible to use a uniform neutralizing
background charge in PME to compensate for a system with a net
background charge. There is probably nothing wrong with this in
principle, because the uniform charge will not perturb the dynamics.
I'd like to comment that, this is tricky business. If your charges are
spread out homogeneously it may be OK, but in practice this is often not
the case (e.g. side chains on a protein). One should try to avoid this
if at all possible.
Oh, this is very bad news. Could you elaborate on that? (I have a CG
model where this would be badly needed).
Further info I found with a lazy check on gscholar:
http://bit.ly/hzzvEx
"Although the stability of a trajectory is a necessary condition for
studying equilibrium observables of a molecular system, it is not a
sufficient one to guarantee their correctness. The use of lattice
summation methods implies that periodicity in a system simulated under
periodic boundary conditions is considered to be an intrinsic property
of this system. We refer to this choice as Ewald boundary conditions
(EWBC). There are a number of reasons to expect that the use of EWBC for
simulating solutions may lead to undesirable side effects. [...]
Finally, when a non-neutral solute is considered, the use of EWBC
implicitly introduces a homogeneous background charge that neutralizes
the unit cell. This charge density will not model realistically the
charge density arising from a counter-ion atmosphere, because (i) it
overlaps with solute atoms; (ii) it is independent of the distance to
the surface of the solute molecule; and (iii) it completely neutralizes
the solute charge within an arbitrary volume of solution, the volume of
the unit cell."
I would love to know how the way GROMACS does PME compares with this...
thanks!
m.
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