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

From: David A. Case <>
Date: Mon, 16 Oct 2006 15:33:14 -0700

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.


The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Wed Oct 18 2006 - 06:07:20 PDT
Custom Search