From: Hadi Dinpajooh (mdinpajo_at_asu.edu)
Date: Thu Aug 01 2013 - 13:39:42 CDT
The PSF file contains information about q_D, polarizability (alpha),
lone-pairs, thole parameter, etc., but it does not contain any information
about force constant. You should add force constant information to the
parameter file when you run NAMD simulations. You do need to calculate the
force constant, k_D, for given values of alpha and q_D. However, you can
calculate q_D for given values of alpha and k_D instead (I believe this is
how CHARMM generates PSF files). If you use a very stiff force constant,
then the displacement of the Drude particle remains much smaller than any
interatomic distance. Also note that if you want to use a force constant of
1000 kcal/(mol Ang^2), you should set it to 500 kcal/(mol Ang^2) in the
parameter file due to the potential function used for bond stretches, i.e.
V(bond) = Kb(b - b0)**2.
Arizona State University
On Thu, Aug 1, 2013 at 4:48 AM, Frank Haverkort <f.haverkort_at_rug.nl> wrote:
> I'm preparing to use the Drude FF for my simulations. Because I don't
> have access to the CHARMM program (which can generate Drude PSF files), I
> want to write a script which makes the Drude PSF file using as input the
> corresponding non-Drude PSF (which VMD can make for me). Now it seems that
> I need to supply reduntant parameters for the Drude polarizabilities, and
> I'm wondering if my understanding of this is correct.
> In the PSF file, the drude charge q_D and the polarizability alpha are
> specified. On the other hand, the force constant for the drude particle k_D
> is specified in the force field parameter file. But since these quantities
> are related via alpha = q_D^2 / k_D, why is it not sufficient to define
> only two of them in the input files? Now it seems that I manually have to
> calculate the force constant k_D from a given alpha and q_D.
> Furthermore, I found a contradictory statement in the Drude documentation
> of the NAMD website (http://www.ks.uiuc.edu/Research/Drude/):
> The force constant **kD**, which is assumed to be the same for all atoms
> without any loss of generality in the value of alpha**al**
> This statement seems to contradict the statement I found on this mailing
> list, that the Drude force constants are specified in the force field
> parameter file. In that file, I have observed that you can indeed
> seperately set the bond force constant for each combination of two atom
> types. Is this an error on the side of the documentation, or am I missing
> Hope any of you can clarify this!
This archive was generated by hypermail 2.1.6 : Tue Dec 31 2013 - 23:23:31 CST