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

Berk Hess hess at kth.se
Wed Mar 4 18:50:24 CET 2015

On 03/04/2015 06:35 PM, David van der Spoel wrote:
> 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.
I wouldn't agree with this. The Hamiltonian is well defined and you do 
sample a Boltzmann distribution. But the Hamiltonian and distribution 
might be very different from the "correct" Hamiltonian. GB and RF are 
effective free-energies, as averaged over certain conditions. If the 
conditions you use them in are different from the conditions used to 
derive the potential (free-energy), than your results might differ (be 
wrong) a bit or a lot.


>> 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

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