all atom simulations with explicit water molecules and langevin thermostat

From: Margaret S. Cheung (mscheung_at_uh.edu)
Date: Thu Oct 04 2007 - 16:28:14 CDT

Hi,

I thought that langevin dynamics is to approximate solvent dynamics
implicitly. In the NAMD script setting of all-atomistic simulations, the
langevin thermostat is turned on even explicit water molecules are
included. Could someone please shed light on me as I was confused by
this configuration? We ran all-atom simulations with and without
langevin thermostat and the energy distribution from both looked
different. Did user normally include langevin thermostat for all-atom
simulations with explicit water molecules? I google this question but
without much success in return. If someone has links to refer answers to
this question, please kindly let me know, too.
Thank you.
Sincerely,
Margaret Cheung

-- 
Margaret S. Cheung
Assistant Professor
Department of Physics
629C Science and Research 1
University of Houston
Houston, TX 77204-5005
email:   mscheung_at_uh.edu
(O)713-743-8358 (F)713-743-3589
http://www.phys.uh.edu/~mscheung/

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:45:20 CST