[gmx-developers] Reaction Filed crash!
baptista at itqb.unl.pt
Mon Dec 19 02:11:42 CET 2011
On Sun, 18 Dec 2011 16:21:34 +0100, David van der Spoel wrote:
> On 12/18/11 12:48 AM, baptista at itqb.unl.pt wrote:
>>>> We can also discuss if, as a general rule, using a continuum
>>>> field is better or worse than using a lattice method such as PME,
>>>> is a different issue. Like many other people (Wilfred van
>>>> Warshel, Alan Mark, Philippe Hünenberger, etc), I'm really not
>>>> that lattice methods offer any real advantage, because I find the
>>>> published evidences for either their benefits or their artifacs to
>>>> rather weak or contradictory.
>>> For HOMOGENEOUS systems, then I agree; the configurations sampled
>>> can be
>>> achieved by cheaper methods than PME -- basically, the
>>> configurations are
>>> dominated by short-range effects, and beyond a certain range, all
>>> extra interactions do is affect the overall energy, which can be
>>> pretty well by many methods (including reaction field).
>>> When lattice methods are needed is inhomogeneous systems, such as
>>> and interfaces, because the long range order affects the
>>> sampled, and RF and other continuum methods simply can't handle
>>> properties will depend on cutoffs, etc.
>> Indeed, the symmetry of those systems is totally different and much
>> in line with a lattice model than with a a spherical isotropic RF.
>> Still, the artificial periodicity along the normal to the interface
>> sometimes lead to strange effects, as in the case of a charged
>> (charged lipids and/or adsorbed counterions). We know that the
>> field should not decay as you move away from one of the monolayers
>> (charged plate), because the oblique contributions from the infinite
>> surface exactly cancel that decay -- a somewhat counter-intuitive
>> due to the long-ranged order effects that you mention, and which
>> never be captured by a standard RF. However, in addition to
>> realistically mimicking the infinite interface, a lattice model also
>> places in the normal-oriented boxes a parallel copy of the oposite
>> similarly charged monolayer, so that the field in the solvent region
>> would cancel (two identically charged parallel plates), and so we
>> the constant field that is so typical of a charged interface... So,
>> lattice models seem a mixed blessing in this case. Actually, we are
>> currently considering and testing alternative approaches to use with
>> charged membranes, so any thoughts are welcome.
> If you have a charged membrane with sufficient counter ions (and
> salt) you have a dipolar system and the field will fall off with
> distance from the membrane, if you leave out the counter-ions it will
> remain constant. Using PBC the field will be enhanced artificially.
> have derived an analytical relation for this effect in the supporting
> information of this paper: http://dx.doi.org/10.1002/anie.200703987
> Your best bet is to establish using PME and counter-ions how large
> the PBC effect is, then you can probably change the epsilon_surface
> slightly to reduce the effect. The exact value should depend on the
> box size. I have not tried this myself though.
Sorry, I should have been more clear. Naturally, the addition of ions
will lead to a distance-dependent field (Gouy-Chapman, etc). My point
was that the lattice method creates a wrong physical model to start
with. So, if you think of the electrostatic effect of adding the ions in
terms of a Debye (not Guntelberg) charging process, the initial state
would be completely wrong, which is not particularly encouraging...
Anyway, I must look at the paper you mention. Thanks also for the
suggested approach, which is similar to some we are considering.
> David van der Spoel, PhD, Professor of Biology
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596, 75124 Uppsala, Sweden
> phone: 46 18 471 4205 fax: 46 18 511 755
> spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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