[gmx-users] how to simulate at a specific dielectric constant
David van der Spoel
spoel at xray.bmc.uu.se
Wed Nov 15 11:55:20 CET 2006
Qiao Baofu wrote:
> Hi David,
> There is not a simulation parameter that you can change that will
> influence the dielectric constant of your system.
> I don't grasp this. If the system has two fluid, one as solute, another
> as solvent. I had thought that I should change the value epsilon_r in
> the .mdp file from the default 1 to some other value. Is it wrong?
Yes. If you change epsilon_r the Coulomb interaction will be scaled but
not the Van der Waals. Hence the balance of forces is disturbed and you
system will implode (epsilon_r < 1) or explode (epsilon_r > 1). You are
probably thinking of implicit solvent methds where this might apply, but
these are not implemented in GROMACS.
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
More information about the gromacs.org_gmx-users