From chemistry-request%!at!%server.ccl.net Sat Nov 17 12:00:37 2001 Received: from gandalf.cber.nih.gov ([128.231.52.5]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fAHH0aB29449 for ; Sat, 17 Nov 2001 12:00:36 -0500 Received: from localhost (rvenable |-at-| localhost) by gandalf.cber.nih.gov (980427.SGI.8.8.8/980728.SGI.AUTOCF) via ESMTP id LAA27714; Sat, 17 Nov 2001 11:55:26 -0500 (EST) Date: Sat, 17 Nov 2001 11:55:26 -0500 From: Rick Venable To: Ibrahim Moustafa cc: chemistry: at :ccl.net Subject: Re: CCL:Velocity re-assignment In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII There are several methods and reasons for modifying MD velocities: + periodic assignment during equilibration for NVE dynamics + periodic scaling during equilibration for NVE dynamics + changed every timestep, coupled to a piston for NVT dynamics NVE and NVT refer to constant volume ensembles, with explicit conserved system Hamiltonians; velocities are not changed during NVE dynamics, but 100 ps or more of equilibration with velocity adjustment is usually needed to get a system w/o large temperature drift. One should not include the equilibration time period in the calculation of molecular properties. The use of a piston to "extend" the system (adding degrees of freedom) is often used to provide true NVT dynamics; the potential and kinetic energy of the piston are included in the system Hamiltonian. The same method can be applied to NPT (const T,P) and NPH (const P) ensembles in a rigorous way, from the viewpoint of statistical mechanics. I should note that a method termed "weak coupling", popularized by HC Berendsen's implementation, has also been used for constant T simulations; a theoretical issue with that approach is that the ensemble isn't known, and hence neither is the Hamiltonian. The extended system approach is preferred, due to the rigorous stat mech ensemble. There's a more complete discussion of these issues in: "Computer Simulation of Liquids", MP Allen and DJ Tildesley, Clarendon Press, Oxford UK (1987; pbk 1989,1990). Feller, Zhang, Pastor & Brooks, JCP, 103, 4613 (1995) The JCP paper discusses the extended system implementation for constant T and/or constant P in CHARMM, and compares it to the weak coupling algorithm. On Fri, 16 Nov 2001, Ibrahim Moustafa wrote: > I'm doing MD on my protein structure; in some recent work on > simulation using MD at const. temp. I've seen people re-assign velocities > every certain Intervals. > > I want to know excactly how to re-assign velocities periodically? > Is it by changing the seed value randomly periodically? or they use > another way to do that? > > What are the benefits for the simulation from velocity re-assignment? > Doesn't this drift the trajectory everytime velocities being > reassigned?? Is this good for simulation? > > I'd be appreciated if anyone calrify this point. > > I use Tripos software to do the simulation. =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+= Rick Venable 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 =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=