AMBER Archive (2003)

Subject: Re: AMBER: GIBBS - PMF question: How to get <dV/d_lam> during TI calculations?

From: David A. Case (case_at_scripps.edu)
Date: Tue Dec 23 2003 - 13:18:39 CST

On Mon, Dec 22, 2003, Jiri Matousek wrote:

> I am using PMF method in gibbs with TI (CF). I am trying to find how
> many steps is necessary for sampling (after quite long equilibration
> (500ps)). I think it will be clear from chart <dV/d_lam> vs ps (of
> sampling).
> Is there any simple way how to get values of <dV/d_lam> during
> calculation (window)? I have isande=1, but this gives me <dV/d_lam> only
> after each window.
>

This is just a guess (since I don't use gibbs anymore): can you use a larger
number of smaller "windows"? That way you could get the <dV/d_lam> values
at a finer grain of time resolution.

..good luck...dac 

-- 

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David A. Case                     |  e-mail:      case_at_scripps.edu
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
10550 N. Torrey Pines Rd.         |  home page:                   
La Jolla CA 92037  USA            |    http://www.scripps.edu/case
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