[gmx-users] creating a solvent box

This may very well be a simple problem, but I have found little in the way of documentation that helped me get it to work: I'd like to form a box (4x6x4 nm^3) filled with 3200 water molecules. I'd like to use the water model specified in sw.itp (polarizable & flexible). In the working directory I

[gmx-users] New shell water model, tabulated bonding interactions, and the documentation.

Over the past couple days I've attempted to implement the water model developed by Ishiyama & Morita (J. Phys. Chem. C 2007, 111, 721-737) using a combination of the shell polarization technique and tabulated potentials for the bonded terms, among other things. Before elaborating below, the documen

[gmx-users] Ion Polarizability (Shell Model)

or using DFT methods, but still don't know how to translate that into a force constant or shell-particle charge. thank you, ~Eric Shamay ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please s

[gmx-users] Adding polarizability

e. Is that all I need to do, or is there a missing or incorrectly done step before I can actually use the flexible SPC? Lastly, I would also like to use the anharmonic (cubic) term for the OH stretching as per ferguson. What do I need to do to enable this? Thank you, -- ~Eric Shamay ___