From owner-chemistry[ AT ]ccl.net Tue Nov 29 21:48:00 2005 From: "Rick Venable rvenable|*|pollux.cber.nih.gov" To: CCL Subject: CCL: Langevin Dynamics Message-Id: <-30114-051129213805-15312-8mhwW3QmsZAdOCMVRPU8hg+*+server.ccl.net> X-Original-From: Rick Venable Content-Type: TEXT/PLAIN; charset=US-ASCII Date: Tue, 29 Nov 2005 21:35:59 -0500 MIME-Version: 1.0 Sent to CCL by: Rick Venable [rvenable*|*pollux.cber.nih.gov] On Tue, 29 Nov 2005, Bob Johnson robertjo%%physics.upenn.edu wrote: > Hello everyone, I am simulating a single stranded DNA molecule > adsorbing to a carbon nanotube. I've conducted simulations with > various amounts of water ranging from complete hydration to complete > vacuum. I have also looked at how the DNA conformation about the > nanotube changes upon removing water. It seems that the water > effectively screens the DNA base-tube interactions. Removing the water > allows the DNA to form a tighter conformation about the nanotube. > > Since, ultimately, I am interested in the DNA conformation about the > nanotube in vacuo, would using Langevin dynamics for the adsorption > process be useful? Thanks, > > Bob Johnson Yes and no; Langevin dynamics models solvent collisions, so the choice of a collision frequency affects the amount of damping. The use of underdamped systems (low collision frequency, 2/ps) has been shown to allow more torsional transitions per timestep than vacuum MD or Langevin dynamics at larger collision frequencies. This allows sampling more conformations in a given simulation. See: Loncharich RJ, Brooks BR, Pastor RW. Langevin dynamics of peptides: the frictional dependence of isomerization rates of N-acetylalanyl-N'-methylamide. Biopolymers. 1992 May;32(5):523-35. However, there's still the issue of electrostatics; an implicit solvent method may be needed to help get the correct DNA:nanotube binding constant. There's also the issue of screening the phosphates > from each other; an increased dielectric is one approach. ------------------------------------- Rick Venable 29/500 FDA/CBER/OVRR Biophysics Lab 1401 Rockville Pike HFM-419 Rockville, MD 20852-1448 U.S.A. (301) 496-1905 Rick_Venable AT nih*gov ALT email: rvenable AT speakeasy*org -------------------------------------