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.
________________________________________________________________________
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
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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