AMBER Archive (2005)

Subject: Re: AMBER: linit in mm-pbsa

From: Ray Luo (rluo_at_uci.edu)
Date: Thu Apr 07 2005 - 23:30:06 CDT

>
>
>> 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,

Hi Fabien and Arantxa,

If you use PBSA for your PB calculations, the convergence is usually
reached before linit, usually less than 100 for typical systems. So
whatever linit you use should not matter. However, if the number of
iterations required is equal to linit as shown in the output file, you
should increase linit. This happens if your systems are very large.

This is different from using Delphi for PB calculations, which almost
always reaches linit, so the Delphi energy does dependent on linit a bit.

>> 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....
>
This is correct. Please check the iteration number in the printout to
make sure it is less than linit.

Best,
Ray 

-- 

====================================================
Ray Luo, Ph.D.
Department of Molecular Biology and Biochemistry
University of California, Irvine, CA 92697-3900
Office: (949)824-9528         Lab: (949)824-9562
Fax: (949)824-8551          e-mail: rluo_at_uci.edu
Home page: http://rayl0.bio.uci.edu/rayl/
====================================================

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