From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Tue Jun 26 2007 - 09:38:17 CDT
Hi Audrey,
for point 1, yes, the barostat/thermostat are forcefield independent;
they will apply forces to the system based on factors such as the
selected temperature and velocities of atoms, but the same thermostats
are used with several different forcefields. Most people using NAMD use
the CHARMM series of forcefields, but there are exceptions.
For point two, it's the opposite... the pressure control methods in NAMD
are used in simulations with explicit solvent. Both of these methods
work by varying the size of the periodic cell to equilibrate it with a
bath of a target pressure, and the interactions of the solvent molecules
are important here. Also, NAMD doesn't have any sophisticated implicit
solvent models (although that will hopefully be changing soon), so for
right now you're stuck with explicit water anyway ;-)
As you get started with this, I'd highly recommend reading the NAMD
paper (JCC 26:1781-1802 2005) and a textbook on molecular modeling (I'm
partial to the one by Andrew Leach) to get a better feel for how things
like NAMD work.
Peter
Audrey Salazar wrote:
> Hello,
> 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?
>
> Thank you.
>
> Audrey
> --
> 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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