AMBER Archive (2006)

Subject: Re: AMBER: How to find equillibration time for my system in a generalised born solvation model

From: David A. Case (
Date: Mon Oct 16 2006 - 17:33:14 CDT

On Tue, Oct 17, 2006, Gobind Singh Bisht wrote:

> I have a 42 bp DNA implicitly solvated with generalised born
> solvation model ( igb=1) using the Langevin thermostat... I want to study
> the system under changing temperature conditions. How do i find the minimum
> time required for equilibration of my system before i can get a production
> MD trajectory and the system is ready for a second phase of temperature
> change and so on..

Basically, plot the instantaneous temperature vs. time and look for a plateau
(in which will be a pretty noisy signal). Equilibration will be very fast
for a Langevin thermostat -- 50 psec should be plenty.

> another question is how exactly is
> the thermostat coupled to the GB solvation scheme... can anyone refer some
> papers to me where i can get a look at the analytical equations for this
> implementation??

Literature references are given in the Amber manual; refs. 68 and 69 give
the equations used, along with an analysis.

> Also Langevin Dynamics implementation as such has a viscous
> term associated to it whereas in implicit solvation there is no viscosity

The implicit solvent *energy* term (i.e. GB) has no intrinsic viscosity;
the viscosity is a dynamical effect which is represented by the collision
frequency in Langevin dynamics.


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