[gmx-developers] Reaction field questions (David van der Spoel)

David van der Spoel spoel at xray.bmc.uu.se
Wed Mar 4 18:35:27 CET 2015

On 2015-03-04 17:18, Noel Carrascal wrote:
> David,
> You asked:
>>These forces are used to compute the virial and hence the pressure.
>>Having said that, if you are interested in improved methods for long
>>range forces, why are you looking at reaction fields?
> I am interested in isotropic liquids and crystals.  In particular,
> phase transitions of pure liquids without liquid-solid and liquid-vapor
> coexistence(if such think is possible). Under these conditions, reaction
> field
> methods give results comparable to Ewald summations at a fraction of the
> computational cost.

It depends what you call comparable. You may want to check e.g.
Matthias et al. JCP 118 (2003) 10847--10860 who suggest a 4 nm cutoff 
may be needed, or my own work JCTC 2 (2006) 1-11.

I have been thinking a bit about these things lately and come to the 
following (preliminary) conclusion:
In general, any method that replaces part of the potential by an 
averaged force, like an implicit solvent model, or a coarse grained 
model, uses an ill-defined Hamiltonian. Ill-defined since it contains in 
part the entropic effect of the part left out. That means time becomes 
meaningless, and one is not sampling a Boltzmann energy surface anymore. 
Not sure if RF falls in this category too, but I think so.

> To give you a little bit more context, in case you are curious, I am
> interested in
> reproducing and understanding in more depth the problem & debate
> presented in the following
> article:
> http://physicsworld.com/cws/article/news/2013/mar/26/why-water-prefers-the-single-life
> Down the road, I would like to apply what I learn to improvements for
> long range methods
> in the simulation of larger biomolecules an other non-isotropic system.
> Reactions fields
> is just the beginning.
> Also, I am running a small test, and the forces given by gromacs differ
> from my own calculations
> for a simple water system using a simple R script. I assume I am missing
> something. It is probably
> the cut-off scheme that Berk mentioned.
> Thanks for your response
> Noel Carrascal

David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se

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