String method in collective variables: minimum free energy paths and isocommittor surfaces.
A computational technique is proposed which combines the string method with a sampling technique to determine minimum free energy paths. The technique only requires to compute the mean force and another conditional expectation locally along the string, and therefore can be applied even if the number of collective variables kept in the free energy calculation is large. This is in contrast with other free energy sampling techniques which aim at mapping the full free energy landscape and whose cost increases exponentially with the number of collective variables kept in the free energy. Provided that the number of collective variables is large enough, the new technique captures the mechanism of transition in that it allows to determine the committor function for the reaction and, in particular, the transition state region. The new technique is illustrated on the example of alanine dipeptide, in which we compute the minimum free energy path for the isomerization transition using either two or four dihedral angles as collective variables. It is shown that the mechanism of transition can be captured using the four dihedral angles, but it cannot be captured using only two of them.
Maragliano
Luca
L
Courant Institute of Mathematical Sciences, New York University, New York, NY 10012, USA. maraglia@cims.nyu.edu
Fischer
Alexander
A
Vanden-Eijnden
Eric
E
Ciccotti
Giovanni
G