From: David Hardy (dhardy_at_ks.uiuc.edu)
Date: Thu May 06 2010 - 18:12:58 CDT
Files sent off-list.
-Dave
On May 6, 2010, at 5:35 PM, Igor Petrik wrote:
> 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/
>>
>>
>>
>>
-- 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/
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:55:45 CST