From: Igor Petrik (petrikigor_at_gmail.com)
Date: Thu May 06 2010 - 17:35:20 CDT
David,
Thanks for the info! Just one request, would you happen to have a
sample 'extended PSF' in which drude is enabled?
Thanks again,
- Igor Petrik
University of Illinois, School of Chemical Sciences
Department of Chemistry
CLSL A325, Box 74-5
600 S Mathews
Urbana, IL 61801
On Sat, Feb 20, 2010 at 11:17, David Hardy <dhardy_at_ks.uiuc.edu> wrote:
> Hi Igor,
> 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 oscillators
> 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.
> Best regards,
> Dave
>
> 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"
> interactions.
> 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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