PROFASI  Version 1.5
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minimize Class Reference

Minimize an expression over degrees of freedom of a protein molecule. More...

#include <minimize.hh>

Detailed Description

The program minimize uses conjugate gradient minimization to minimize a given observable or a linear combination of observables near a given structure. Typically this program is used with both settings file and command line options together. For instance, if we have the following settings file:

set_population testprot.pdb::A
new_obs ProteinRMSD rmsd using +HV ; struc1 testprot.pdb::A ; struc2 $::A
new_obs Rg rg

One can then minimize an arbitrary linear combination of the defined observables, like this:

minimize "Etot+25*rg+10*rmsd"

Etot in the above example is the total energy, which is an implicitly defined observable, even if it is not created with a "new_obs" command. Similarly, the component terms of the energy function can be used without their explicit declaration in the settings file.

Minimization can be restricted to only the side chain degrees of freedom with the option –using.

minimize "Etot+25*rg+10*rmsd" --using "sc" "*"

The –using option takes 2 parameters. It is –using what where . The first argument could be "bb", "sc" or "all", for backbone, side chain and all degrees of freedom. The second argument is a selection inside the population where the degrees of freedom will be varied. For instance,

minimize "rg" --using "all" "A/15/56"

will minimize the observable rg using all degrees of freedom in chain A for group indices (start from 0, include capping groups) 15 through 56.

The output of the minimize program is stored in a file called output.xml in PROFASI's XML structure file format .

See Also
Regularization: approximating a protein structure , PROFASI's XML structure file format, Table of contents

The documentation for this class was generated from the following files:

PROFASI: Protein Folding and Aggregation Simulator, Version 1.5
© (2005-2016) Anders Irbäck and Sandipan Mohanty
Documentation generated on Mon Jul 18 2016 using Doxygen version 1.8.2