file:///home/jhenin/Documents/Web_eDAM/ABF/glpf-small.gif   adaptive biasing force
 
Overcoming free energy barriers in molecular simulations using an average force
 


Historical background

Theoretical foundations
References
Success stories
Repository
Contact us


NOTE: the code provided here is obsolete as of NAMD 2.7b1. The newer implementation, integrated in the NAMD binary, offers all previously available functionality and much more. This page is provided only for backwards-compatibility purposes.


Repository


The NAMD ABF code consists of a suite of Tcl modules, readily available in the NAMD distribution. The current official version of the ABF code includes a limited number of order parameters. Yet, upon requests of end-users, new order parameters are being developed and will be ultimately added to the upcoming version of NAMD. In the meantime, these new order parameters are being made available to the public for testing purposes.

Currently available order parameters include:

distance
corresponds to the distance separating two selected atoms:

abf1: index of the first atom of the reaction coordinate;
abf2: index of the second atom of the reaction coordinate.




distance-com
corresponds to the distance separating the center of mass of two sets of atoms, e.g. the distance between the centroid of two benzene molecules:

abf1: list of indices of atoms participating to the first center of mass;
abf2: list of indices of atoms participating to the second center of mass.




abscissa
new

The distance between the centers of mass of two sets of atoms along a given direction. The word direction denotes a vector, i.e. a Tcl list of three real numbers, defining the direction of interest:

abf1: list of indices of atoms participating to the first center of mass;
abf2: list of indices of atoms participating to the second center of mass.
abf3: list of indices of atoms forming the system that moves along the vector defined by abf1 and abf2.



zCoord
The distance separating two groups of atoms along the z-direction of Cartesian space. This reaction coordinate is useful for the estimation of transfer free energies between two distinct media:

abf1: list of indices of reference atoms;
abf2: list of indices of atoms of interest  - e.g. a solute.




zCoord-1atom
This order parameter is similar to zCoord, but using a single atom of interest:

abf1: list of indices of reference atoms;
abf2: index of an atom of interest


  

xyDistance
The distance between the centers of mass of two atom groups, projected on the (x, y) plane:

abf1: list of indices of atoms participating to the first center of mass;
abf2: list of indices of atoms participating to the second center of mass.




gyration
new                                 

The radius of gyration of an ensemble of atoms.

abf1: list of indices of atoms participating to the computation of the radius of gyration.



dihedral
new

The dihedral angle formed by a sequence of four atoms:

abf1: list of indices of the four atoms defining the torsion.