On 30/01/11 16:13, David van der Spoel wrote:
On 2011-01-30 17.08, ms 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).
With homogeneous I mean a solution of ions.
Hmm, I would be happy to have more informations -that is, *why* should
one try to avoid this? What artefacts/problems should I expect?
Here:
http://bit.ly/ig11UQ
it seems that people use PME -with CHARMM here- to model efficiently
non-neutral systems:
"As a result of including only the ion of interest in our simulations,
the system will have a non-neutral charge. With particle-mesh Ewald
electrostatics, this will result in a uniform neutralizing plasma [29]
and [30]. In other words, a homogeneous neutralizing background charge
is implicitly applied to the entire simulation space to avoid the
divergence of the Ewald sum and to neutralize the system [29] and [30].
Although the background charge will alter the free energy profile, its
effect can be shown to be negligible for a non-neutral charge of 2 e.
The offset of the electrostatic free energy can be determined from [30]
M.A. Kastenholz and P.H. Hünenberger, J. Phys. Chem. B 108 (2004), p.
774. Full Text via CrossRef | View Record in Scopus | Cited By in Scopus
(58)[30]"
Of course they may be horribly wrong, but they list some literature in
support (which I'm going to check, but meanwhile...)
Can spreading neutralizing charges along the other chain atoms be a
viable alternative for enough atoms and enough low charge? (e.g. if I
have 100 atoms and a +5 net charge, adding a -0.05 charge on all others?)
Sounds like a recipe for disaster.
Uhm, given that mine is already a coarse-grained systems where
practically all particles have 0 charge it could indeed change things
badly. I've read this idea on one of the links of the mailing lists
linked above in the thread.
Try looking for solutions with
explicit counter ions.
That's exactly the point: I desperately need to *avoid* explicit counter
ions. I don't want interactions between my systems and "fake" counterions.
Thanks a lot,
Massimo
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