[gmx-users] emtol

Nguyen Hoang Phuong phuong at theochem.uni-frankfurt.de
Fri Jan 17 12:37:26 CET 2003

On Fri, 17 Jan 2003, [iso-8859-1] Tanos C. C. França wrote:

> 	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 ?

I usually perform em for systems of protein and water and I can reach to
Fmax = 0.001 using cg with emstep = 10^{-6} and double precision. Usually
the annealing simulations are done and then the em are performed for the
obtained configurations.


> 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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