On Fri, Jun 10, 2016, conor parks wrote:
> I
> checked the radial distribution function of the methyl carbon-methyl carbon
> (c3-c3), and noticed longer tails than I expected. I thought, perhaps
> naively, that the RDF should converge to 1 at 12.0 nm, as I believe this is
> the cut off for the GAFF force field.
First, the GAFF force field doesn't have a cutoff; your simulation will
have no electrostatic cutoff, and a Lennard-Jones cutoff specified by the
value of "cut" in your MD input file.
Second, convergence of RDF's is not directly related to force field cutoffs
in any event. You could have RDF's that decay to zero at lengths lower than
or larger than the cutoff, depending on the nature of the forces.
Third, if you are concerned about convergence, run longer simulations to see
what happens, (or separately analyze different parts of the simulations you
have.)
Finally, be careful about the densities you are using. 0.4 g/cc doesn't sound
like a density that would be appropriate for an acetominiphen/water mixture,
although once you are above the boiling point of (pure) liquid water, I suppose
anything could be appropriate. TIP3P water is probably not a very good
model for water at those conditions. Check how the density changed as you
moved to an NPT simulation: did you get what you were expecting? If you
really want to simulate systems at 380K and 1 atm pressure, I suggest gaining
experience with a pure water simulation first, before adding any solutes.
....good luck....dac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sat Jun 11 2016 - 10:30:02 PDT
