[gmx-users] energy minimization of a charged system in vacuum

devicerandom devicerandom at gmail.com
Wed Feb 2 18:43:37 CET 2011

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?


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 

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,

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