[gmx-users] uniform dielectric constant

David van der Spoel spoel at xray.bmc.uu.se
Wed Jul 18 19:47:56 CEST 2007

Mikael Lund wrote:
> Reading the mailing list and the wiki as well, I see that GROMACS has 
> little support for implicit solvent. However, I'm interested in 
> simulating charged polymers (small spheres connected with springs) in an 
> aqueos salt solution (more spheres). Assuming no dielectric boundaries 
> -- i.e. a uniform dielectric continuum -- I thought of setting epsilon_r 
> to 80. Clearly the dynamics will be wrong but I'm interested in static 
> properties only. Do you see any pitfalls with this approach?
if the potentials are optimized for this it may work, but you probably 
want to read recent polymer literature. Berk Hess has two relevant 
papers in 2006 (one PRL, one JCP) that are done predominantly with GROMACS.
> Best,
>   Mikael
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
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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