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.
________________________________________________________________________
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
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