AMBER Archive (2008)

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

From: Reena ..... (ren.saini_at_gmail.com)
Date: Wed May 28 2008 - 00:34:39 CDT

hello,

I am too new to amber. Just read your query and answer to it by Dr. Case. I
didnt understand the last part of the answer
" You are right to be worried about the random part: be sure to select a new
random number seed for each restart."
New random no. seed for each restart????? what does this mean?
Please elaborate more on it.

regards

A curious student.....:)

On Wed, May 28, 2008 at 10:29 AM, David A. Case <case_at_scripps.edu> wrote:

> 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
>
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