Amber users,
I am currently attempting to model a simple 1M NaCl aqueous solution with Amber. I have tried this multiple times to no avail, using different ensembles, creation methods via tleap, xleap, pdb, and--when using leap--both with and without using the LEaP 'addions' command. However, all of the simulations turn out the same. Both the sodium and chloride ions show a tendency to remain in same-charged groups. As in, both of the sodium and chloride ions tend to form groups of about 3 of the same type of atom. I have tried minimizing the energy for large amounts of time, and the ions all start out well solvated. I have used parm99.dat, frcmod.ff99SB, and manually adding the force field, vdw, and charge parameters myself. I'm pretty sure that it is a simple error that I've been overlooking and all help is appreciated.
Logan H. Eckler
Research Assistant
Western Kentucky University
Department of Chemistry
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Received on Tue Jul 10 2012 - 14:30:03 PDT
