On Tue, Jul 10, 2012, Eckler, Logan, H wrote:
> 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.
Well, parm99.dat has a set of force field parameters that are 13 years
old, and are known to have bad behavior, especially at higher concentrations.
Please see the section on "Ions" in Chapter 2 of the AmberTools reference
manual. This will show you how to load more recent ion parameters that avoid
this problem. (The ion parameters depend on which water model you are
using, as described in the reference manual.)
...dac
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Received on Tue Jul 10 2012 - 15:30:03 PDT
