Langevin Dynamics again

From: Wei Fu (
Date: Thu Feb 19 2004 - 15:23:22 CST

Hi, Jerome,

     I am doing Langevin Dynamics with NAMD and have some questions about Langevin Dynamics.

     1. Based on what you said, and the equation in the tutorial, the Langevin Dynamics is equal to Stochastic Dynamics in NAMD?

     2. You said, people usually do Langevin dynamics with a rather small friction coefficient with NAMD. And in the user-guide, the langevinDamping usually set to be 1 or 5. While I read some refs, usually people do stochastic dynamics, set the friction coefficient to be 0.1, but in the tutorial, it said a langevinDamping as low as 1. I want to do long time Langevin Dynamics, how come I set "LangevinDamping" to be 0.1 ?

     3. It uses implicit water, what kind of model does it use?

    In fact, I only concern the motion of protein, and would like to do a long-time simulation. You know, the timescale for a biomolecule is from 100ns to several hundred none second, for my protein, it has a unusual shape, it will add too much water to build a periodic box (even build dodecahedron box), so, that is the idea I want to run Langevin Dynamics.

    Look forward to your reply, thanks!


  Wei Fu (Linda)
  Postdoctoral Research Associate
  Department of Biology and Biochemistry
  University of Houston
  4800 Calhoun Rd. HSC #402C

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