[Dock-fans] Simplex minimization

Trent Balius tbalius at aol.com
Sat Sep 26 11:40:09 PDT 2009

 Hi Yasser,

Each vertex is a conformer of your molecule.  It is my understanding that the minimizer takes in one conformer of the molecule (fully or partially grown) and perturbs the molecule to create (N + 6) new conformers. (there are N+7 conformers in total).  Where N is the number of rotatable bonds (internal degrees of freedom) and 6 is the number of translational and rotational degrees of freedom.   The highest energy conformer is then reflected through the hyper plane defined by the other points and is moved to find a new lower energy conformer.  The new highest energy is then reflected through the new hyper plane.  This is continued until the max cycles are reached or until the minimizer converges.

The simplex method is the same whether you are in 3D or in (N+6)D.  In 3D you have a plane defined by 3 points to reflect your highest point through. And (N+6)D you have a hyperplane defined by N+6 conformers to “reflect” the highest energy molecule through

For more information on how to use the minimizer see the DOCK 6 manual:


I hope this helps,

Trent E. Balius
Graduate Student, Rizzo Group,
Department of Applied Mathematics and Statistics,
Stony Brook University.
Office: Math Tower 3-129

-----Original Message-----
From: Yasser Almeida Hernández <pedro.al at fenhi.uh.cu>
To: Dock <dock-fans at docking.org>
Sent: Fri, Sep 25, 2009 3:55 pm
Subject: [Dock-fans] Simplex minimization

Hi all!!0A
In the simplex energy minimization, each vertex represent what?
How match the simplex approach (3-simplex, tetrahedron) with the atom  
coordinates and rotable bonds (torsions) during the energy minimization?
I hope you help me..


Lic. Yasser Almeida Hernández
Center of Molecular Inmunology (CIM)
Nanobiology Group
P.O.Box 16040, Havana 11600, Cuba
Phone: (537) 271-7933, ext. 221

Correo FENHI

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