AMBER Archive (2004)

Subject: AMBER: langevin dynamics

From: Wei Fu (
Date: Sun Mar 21 2004 - 21:22:27 CST

Dear Amber developer,

    We want to do Langevin Dynamics simulation in vacuum on a large
protein (around 1000 residues). From your website, we noticed the langeve dynamics is available to simulate the
solvent frictional effect in the new version Amber 8, which uses implicit
water model -- GB to simulate the solvent effect. You know, our system is pretty big, we want to study the large scale domain motion,
so it is not suitable for running MD simulation in explicit water on such big system. Could you tell
if the Langevin Dynamics in vacuum in amber8 is suitable for our study? If so, we will buy it
immediately. Has anybody have experience on Langevin Dynamics in vacuum? Any hints and suggestions will
highly be appreciated!



  Wei Fu (Linda)
  Postdoctoral Research Associate
  Department of Biology and Biochemistry
  University of Houston
  4800 Calhoun Rd. HSC #402C
  Houston, TX 77204-5001 USA
  Phone:713-743-8355(o) 713-795-9270(h)

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