From: David Hardy (dhardy_at_ks.uiuc.edu)
Date: Sat Feb 20 2010 - 10:17:55 CST
First know that we are still debugging Drude polarizability. Also,
none of our tools yet generate the necessary input files,
particularly the extended PSF. Our collaborators use CHARMM to
generate the input files.
With that said, the new configuration file commands are:
drudeOn - perform integration of Drude oscillators? (yes/
no, no is default)
drudeTemp - (low) temperature for freezing Drude oscillators
drudeDamping - Langevin damping coefficient for Drude
drudeBondLen - Length beyond which to apply quartic
restraining potential to Drude bond
drudeBondConst - Force constant for restraining potential
You must use Langevin with Drude. The integration is performed with
a dual Langevin thermostat to keep the Drude degrees of freedom cold
while keeping everything else at standard temperature.
You should get the most recent build of NAMD.
On Feb 19, 2010, at 6:09 AM, Igor Petrik wrote:
> Hello NAMD Developers/Knowledgeable folk,
> I understand that Drude polarizability is supported by CHARMM (
> http://www.charmm.org/html/documentation/c32b2/drude.html ) and is at
> least partially implemented, though perhaps not "supported" in NAMD;
> however I cannot find much information on implementing Drude
> polarizability through NAMD.
> Could someone list (or point me to a list of) the NAMD parameters
> related to implementation of Drude polarizability, or give an example
> of its implementation? Any help is appreciated.
> To satiate any curiosity, we would like to model "halogen bonding"
> Thank you in advance,
> - Igor Petrik
> University of Illinois, School of Chemical Sciences
> Department of Chemistry
> CLSL A325, Box 74-5
> 600 S Mathews
> Urbana, IL 61801
-- David J. Hardy, Ph.D. Theoretical and Computational Biophysics Beckman Institute, University of Illinois dhardy_at_ks.uiuc.edu http://www.ks.uiuc.edu/~dhardy/
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