[gmx-developers] modifing nonbonded interactions

David van der Spoel spoel at xray.bmc.uu.se
Fri Oct 24 06:17:07 CEST 2008

Mark Abraham wrote:
> Nazish Hoda wrote:
>> To do implicit-water md for a charged system. In the explicit-water md,
>> water is non-uniformly distributed along the molecules. I am trying to 
>> incorporate
>> this effect in my implicit-water simulation.

Author(s): Hess B, Holm C, van der Vegt N
Source: PHYSICAL REVIEW LETTERS    Volume: 96    Issue: 14  Article 
Number: 147801    Published: APR 14 2006
Times Cited: 9     References: 19     Citation MapCitation Map beta
Abstract: We report a new strategy to parametrize effective ion-ion 
potentials for implicit solvent simulations of charged systems. The 
effective potential includes a pair term and a Coulomb term that by 
means of a concentration dependent dielectric permittivity takes into 
account multibody effects. We demonstrate that this approach allows us 
to accurately reproduce the solution osmotic properties and the ion 
coordination up to concentrations of 2.8 M aqueous NaCl.

> PME requires periodicity, which you shouldn't need for implicit-water.
> If you're really wanting to do implicit-water simulation, you should be 
> looking at simulation packages other than GROMACS.
> Mark
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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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