AMBER Archive (2008)

Subject: AMBER: Which is best temperature controlling method

From: sudipta sinha (sudipta.mml_at_gmail.com)
Date: Tue May 27 2008 - 05:25:02 CDT

Hi All,

         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?

warm regards
sudipta

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