(no subject)

From: Mattia Felice Palermo (mattiafelice.palerm2_at_unibo.it)
Date: Wed Oct 21 2015 - 04:07:03 CDT

Dear developers of NAMD,

I am running several simulations of TIP3P-EW water using the new MSM method to evaluate the electrostatic interactions. I then computed the dielectric constant of water but it does not compare well with that obtained using the classic PME method. For the MSM simulation I have only specified the keyword:

msm yes

and left all the default options. The resulting dielectric constants of bulk water (~11k molecule) are 83.3 with MSM and 96.8 with the PME method. Even if the MSM value is closer to the experimental value, the one obtained with PME is in line with the expected value for this specific model of water. Furthermore, I would have expected a similar value for both methods, consistently with the benchmark results published in JCTC 11, 766 (2015).

Then I considered a thin film of TIP3P-EW water on top of an amorphous silica surface (2D periodic). In this case I have specified the following options for the MSM simulation:

cellBasisVector1 57.108000 0.0 0.0
cellBasisVector2 0.0 57.108000 0.0
msm yes
MSMGridSpacing 2.8554
MSMzmin 8.0
MSMzmax 208.0

The grid spacing ensure that a even number of points divides the basis vectors, while the z_min and z_max values are big enough to contain the sample. An harmonic potential wall was also included to contain escaping water molecules. The computed dielectric constant of water is now 258, while in the simulation with PME, the dielectric constant is 91.5. The potential wall was maintained in the PME simulation for better comparison.

Do you have any idea what may be wrong in my simulations using the MSM method?

Thank you very much for the help!

Mattia Felice Palermo - Ph.D.
UniversitÓ di Bologna
Dipartimento di Chimica Industriale "Toso Montanari"

This archive was generated by hypermail 2.1.6 : Tue Dec 27 2016 - 23:21:26 CST