Module meta

Module for all metadynamics backend functionality

Classes

_Backend

CV
base class for collective variable

CVrgyr
Radius of Gyration Collective Variable

CVrgyr_mass
Radius of Gyration Collective Variable

CVrmsd
rmsd collective variable

CVrmsd_symm
rmsd collective variable

CVwhim
whim collective variable

CVzdist0
This collective variable reports an absolute Z-distance from the simulation box origin (Z==0).

CVzdist
This collective variable reports an absolute Z-distance.

CVDist
distance collective variable

CVAngle
A class to define angle collective variable.

CVDihedral
A class to define dihedral collective variable.

CmsModel

A convenience function to see if we're running under job control. If so, return a _Backend object. Otherwise, return None.

Generate part of the config file for metadynamics simulation

Parameters:

meta_def (sea.Sea object) - The content of definition file for collective variables.
model (cms.Cms object @return a string. Exception will be raised if encounting any errors.) - topology file.

Returns the name of the kerseq and cvseq files given a metadynamics definition file

Parameters:

Read config file for metadynamics simulation

Parameters:

meta_def (string) - The content of definition file for collective variables.
model (cms.Cms object @return a Meta) - topology file.

Check distance of the two groups of atoms defined in the atom list

Parameters:

Variables Details

Value:

'''
meta = {
  interval = 0.04
  height = 0.5
  kTemp = 2.4
  name = "kerseq"
  cv_name = "cvseq"
  cv = [
...