Module: pamm

Description	Usage
implementations of the pamm methodology one application of which can be to determine if atoms are hydrogen bonded or not
Authors: Gareth Tribello

Details

This module provides an implementation of the PAMM methodology that is discussed in the papers that are cited below. It also provides methods for using PAMM to determine how many hydrogen bonds each of the atoms in the system participate within. These methods for determining which atoms are hydrogen bonded use the functionality from the adjmat module and thus allow you to calculate an matrix in which element $i,j$ tells you if there is a hydrogen bond between atom $i$ and atom $j$.

Actions

The following actions are part of this module

Tags

MCOLVARF MATRIX COLVAR

MCOLVARF: actions for calculating functions of vectors of colvars MATRIX: action that calculates an adjacency matrix between atoms COLVAR: a function of a set of atomic positions that returns a scalar

Name	Description	Tags
HBPAMM_MATRIX	Adjacency matrix in which two electronegative atoms are adjacent if they are hydrogen bonded	MATRIX
HBPAMM_SA	Calculate the number of hydrogen bonds each acceptor participates in using the HBPamm method	COLVAR
HBPAMM_SD	Calculate the number of hydrogen bonds each donor participates in using the HBPamm method	COLVAR
HBPAMM_SH	Calculate the number of hydrogen bonds each hydrogen participates in using the HBPamm method	COLVAR
PAMM	Probabilistic analysis of molecular motifs.	MCOLVARF

References

More information about this module is available in the following articles:

• P. Gasparotto, M. Ceriotti, Recognizing molecular patterns by machine learning: An agnostic structural definition of the hydrogen bond. The Journal of Chemical Physics. 141 (2014)
• P. Gasparotto, R. H. Meißner, M. Ceriotti, Recognizing Local and Global Structural Motifs at the Atomic Scale. Journal of Chemical Theory and Computation. 14, 486–498 (2018)