Subject: Re: query regarding AMBER energy minimization

From: [email-masked] (Eberhard von Kitzing)
Date: Tue, 31 Aug 1993 09:26:17 +0200 (MET DST)

> 
> Hello everybody, when i do energy minimization using AMBER forcefield
> i frequently get "linmin failure'. Can anybody tell me what is this
> linmin & how to avoid it and what it is? Where from i can get to 
> know minimization algorithms used in AMBER ?Thank you , Neel
> 
Most optimization procedures work in two step. First they try to
estimate a good direction in which the energy is expected to lower
considerably and second it follows this direction and tries to find
the minimum of the energy function along this line (terminus
technicus: line search). Subroutines doing this task are traditionally
called "linmin". 

If you use the single precision version of AMBER, you can probably
avoid this problems by using the double precision version. If not, you
may have located a difficult area with a low gradient.  In this
situation truncation errors start to become a severe problem. If this
is a low energy area you may have found your goal. In the other case
you may use a short dynamics run to leave this area.

For more detail please see my articles:
E. v.Kitzing, Meth. Enzym. (1992) 211, 449-466
E. v.Kitzing, Prog. Nucl. Acid Res. Mol. Biol. (1992) 43, 89-110

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Eberhard von Kitzing
Max-Planck-Institut fuer Medizische Forschung
Jahnstr. 29, D69120 Heidelberg, FRG

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