Thank you! The value of rcut I was referring to was the of the Lenard jones cut off. I am using a cut off for both the lennard jones and the real space coulombic forces. The reciprocal space potion is being handled with a pppm solver ( I am running simulations in lammps, but since the question was about gaff, I brought it here).
The reason I am running at such a high temperature is that I need to prepare a meta stable liquid. 0.4 g/cm3 is below the solubility of acetaminophen of water at 380K, and hence no crystallization should occur. However for production runs, I will implement a step change in the temperature to 290 K, and monitor crystallization. I am using tip3p, as it has been showing to reproduce the enthalpy of solvation well at 290 K.
At any rate, it sounds like I was incorrect in thinking the RDFs should converge to 1.0 by 12 angstroms, and that this could very well happen for a liquid. I really appreciate your thorough response.
Sent from my iPhone
> On Jun 11, 2016, at 1:26 PM, David A Case <david.case.rutgers.edu> wrote:
>
>> 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
>
>
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Received on Sat Jun 11 2016 - 12:00:02 PDT
