[gmx-users] emtol

Tanos C. C. França tccf at epq.ime.eb.br
Fri Jan 17 12:01:10 CET 2003

	Hi folks,

	What is considered a suitable tolerance (emtol) for a energy minimization
of a big dimeric protein  (884 residues) in a water box  ?  In the article
cited bellow, Berendsen said that he performed an em with steepest descent
until a tolerance of 0,01 Kj/mol.nm. How to do this ? In my machine the most
I achieved was 1000 Kj/mol.nm in a water box. The calculation always stops
when the Fmax is about 1000 and gives me the following mesage: "Step size
too small. Converged to machine precision". What does it means ?

Paper: "Completion and refinement of 3-D Homology Models with Restricted
Molecular Dynamics: Application to Tragets 47, 58, and 111 in the CASP
Modeling Competition and Posterior Analysis" - Proteins: structure,
Function, and Genetics 48:593 - 604 (2002)

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