[gmx-users] Droplet vs. vesicle vs. big periodic box vs. implicit solvent

Steven Kirk Steven.Kirk at hv.se
Sun Apr 23 11:11:28 CEST 2006


I would be grateful if anyone on the list could give me the benefit of 
their expertise on the following proposed simulation:

System: 2 amorphous approximately spherical silica particles of diameter 
2.5 nm, each with a net charge of -9e, with about 5 nm spacing between 
their centers of mass, surrounded by TIP4P water and enough Na+ ions to 
neutralize the overall system (probably found near the charged silica 
surfaces). The system temperature would be set at 300K. The idea is to 
watch the particles move towards each other (e.g monitor particle 
COM-COM distance as a function of time) due to VdW forces until stopped 
by the mutual electrostatic repulsion.

To my naive thinking, there are four ways to tackle this:

1. An isolated sphere of water molecules of diameter at least 8 nm, 
centered on the COM of the 2 particles, enclosing both particles, with a 
Coulomb cutoff, VdW cutoff and rlist set to 8 nm.
Disadvantages: slow Coulomb and VdW calculation, possible water ordering 
effects (see recent DvS paper) with large cutoff, water boiling off the 

2. Like 1. , only with the outermost water molecules in the droplet 
frozen in place to form a 'vesicle', hopefully keeping the water from 
boiling off.

3. Particle pair COM centered in a big periodic box (e.g. 12 x 10 x 10 
nm), particle pair aligned along the x-axis, box filled with water. 
Systems arranged so that each particle is closer to every part of its 
immediate twin that to any periodic copies. rvdw also set to 8 nm.
Advantages: gain efficiencies of PME for Coulomb interaction
Disadvantages: Painfully large numbers of atoms, might be possible with 
large parallel computing power

4. Do away with the explicit water molecules completely, using an 
implicit solvent (but, presumably, keeping explicit Na+ ions and 
particles). rvdw set to 8 nm. Any advice on how to do it this way - this 
is unknown territory for me? Any GROMACS tutorials for implicit solvent 
or GB out there?
Advantages: Small number of atoms
Disadvantages: Lose details of particle-water and ion-water interactions 
(but the latter may not be so important, as polarized water models more 
realistic than TIP4P for ion-water interactions and hydration shell 
structure anyway?)

Insight, suggestions and additional options very gratefully received.

Dr. Steven R. Kirk           <Steven.Kirk at hv.se, S.R.Kirk at physics.org>
Dept. of Technology, Mathematics & Computer Science  (P)+46 520 223215
University West                                      (F)+46 520 223299
P.O. Box 957 Trollhattan 461 29 SWEDEN       http://taconet.webhop.org

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