AMBER Archive (2005)

Subject: Re: AMBER: linit in mm-pbsa

From: Arantxa Sanz (aranzazu.sanz_at_uab.es)
Date: Fri Apr 08 2005 - 04:43:22 CDT

En/na Fabien Cailliez ha escrit:

> Dear all,
>
> I have a question about linit variable in mm-pbsa module for PBSA
> calculations.
> How do I have to set this variable ?

I have been running PBSA calcs for a 25 residues helix in an hydrophobic
environment, and tested linit=500, 1000, 5000 and
results seemed to have converged at linit=500 (i.e. no variation in two
significant figures between the respective output files)
Does it sound reasonable? Many thanks for your contibutions,

Arantxa

> Is there any message in the output which indicates that there is a
> problem with the
> number of iterations being too small ?
> I guess I have only to check if the line "Iterations required
> :" indicates less
> than linit, but I am not sure....
>
> Thanks for your answers,
> Fabien
>
Arantxa Sanz, PhD
Laboratori de Medicina Computacional
Facultat de Medicina
Universitat Autònoma de Barcelona
08193 Bellaterra
Catalonia, SPAIN
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