AMBER Archive (2008)

Subject: Re: AMBER: Which is best temperature controlling method

From: David A. Case (case_at_scripps.edu)
Date: Tue May 27 2008 - 23:59:23 CDT

On Tue, May 27, 2008, sudipta sinha wrote:
>
> I am new in the AMBER world and I am using AMBER9. I want to do
> NVT, NPT simulation of a biomolecule in explicit water and I am also
> interested to calculate some equilibrium dynamical properties through
> various types of correlation function. My problem is choosing the best
> algorithm of temperature controlling for such type of analysis. There are
> three different methods included in AMBER9 for temperature controlling.
> 1)NTT=1 weak coupling algorithm (basically a temperature scaling algorithm.
> so it is not a good algorithm)
> 2)NTT=2 Anderson method (A random part is included)
> 3) NTT=3 Langevin dynamics (Here also a random part is included)
> I am worried about the random part. Is the random part deviate the actual
> dynamics? Among them which is the best algorithm for calculating such type
> of equilibrium dynamical quantities? Could anyone suggest me?

The best (really only) way to calculate time correlation functions is to
equilibrate with the thermostat of your choice (usually ntt=3) and then run
NVE simulations. With explicit water, the difference between NVE and NVT on
an equilibrated simualation is quite small.

You are right to be worried about the random part: be sure to select a new
random number seed for each restart.

...dac

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
      to majordomo_at_scripps.edu