From: Audrey Salazar (alsalazar_at_northwestern.edu)
Date: Mon Jun 25 2007 - 18:41:55 CDT
I am a first year graduate student trying to understand the inner workings
of NAMD. I am hoping that someone can shed some light on some aspects of
the MD simulation. My questions this time center around the algorithms and
assumptions of the barostats and thermostats in NAMD.
1) It is my understanding that the barostats and thermostats can be
implemented with any force field. Am I correct in this assumption?
2) To simulate short nucleic acid chains, I intend to use explicit solvent.
It is my understanding that both the Berendsen and the Nose-Hoover Langevin
piston imply continuum solvation. Should I be concerned that assuming
continuum solvation is inconsistent with using explicit solvent?
-- Audrey L. Salazar Amaral Research Group Dept. of Chemical and Biological Engineering Phone: 847.491.2188 Northwestern University Evanston, IL USA
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