Drude polarizable models with namd

From: Ana Celia Vila Verde (acavilaverde_at_gmail.com)
Date: Thu Aug 02 2012 - 11:11:08 CDT

Hi everyone,

I'm trying to implement Drude polarizable models in NAMD and there are
some issues that I don't understand and for which I could not find
enough information in the namd user list or in the available online
resources (e.g. http://www.ks.uiuc.edu/Research/Drude/ and references
therein). Can anyone shed some light on the following:

In the Extended PSF format necessary for Drude models, in the NATOM
record, exactly what parameter goes in column J (see example below,
taken from the webpage on Drude models in Namd) and how are these values
       2 !NATOM
# A B C D E F
          1 BULK 1 SWM4 OH2 ODW 1.71636
15.5994 0 -0.978253 1.30000
          2 BULK 1 SWM4 DOH2 DOH2 -1.71636
0.400000 0 0.00000 0.00000

The webpage on Drude models in Namd indicates that column J contains the
Thole parameter. However, I read the original reference for the SWM4-NDP
water model (Lamoureux et al, /Chemical Physics Letters, /*2006*/, 418/,
245-249) and there they make no mention of Thole polarization for
simulations of pure water. In subsequent references they indicate that
this parameter is a magic 2.6 (e.g. in simulations of benzene, /J. Phys.
Chem. B, /*2007*/, 111/, 2873-2885) for 1-2 or 1-3 intramolecular
interactions. How does one get to the value of 1.3 used in the example

Furthermore, if one wants to simulate, for example, SWM4-NDP water with
divalent cations, one needs to set a Thole parameter for the ion-water
interactions. In the original reference they report a Thole parameter
for each ion-water pair (e.g. for Mg2+ in SWM4-NDP water, this parameter
is 1.51567). How does one incorporate this value in a psf for water and

Thank you all,


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