From: Zhe Wu (zephyrbless_at_gmail.com)
Date: Wed Oct 21 2015 - 14:16:02 CDT
Could you specify how you calculate the dielectric constant? The dielectric constant of TIP3P-EW water is 89 (D. J. Price, C. L. Brooks, J. Chem. Phys. 2004, 121, 10096), while you are getting 96.8 with PME and 83.3 with MSM. You can find the way we calculated the dielectric constant on page 773 of our JCTC paper.
It is very surprising to see a dielectric constant of water to be 258. How is the water structure? With such a large dielectric constant, the water structure should be very unphysical.
Also, could you give us a little bit more details about your VDW cutoff scheme? As reported in TIP3P-EW’s original paper, a model that incorporates a long-range correction for truncated VDW will give a dielectric constant of 76 instead of 89. Are you using the same cutoff scheme for both PME and MSM?
Hopefully, the above helps.
Klaus Schulten's Group,
Postdoc Fellow in NSF's Center for the Physics of Living Cells,
University of Illinois Urbana-Champaign
Beckman Institute, RM 3125,
405 N. Mathews Ave. Urbana, IL 61820
>> 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.
>> Università di Bologna
>> Dipartimento di Chimica Industriale "Toso Montanari"
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