C++ Libraries and Software for Molecular Modeling (Erik Santiso)
Latest change: 06-09-10 - if you just want all the packages use this link: . You can also get a bash script to build all the projects in the right order here .
common: Contains basic types and base class definitions for all the other libraries - a copy of this directory must be in the same path as each one of the libraries below (only one copy is necessary if you keep all the projects in the same directory).
Download: common.tgz
mymath: Contains classes for vector, matrix and quaternion operations, calculation of special functions, sorting, matching problems, root finding, optimization, linear and orientational statistics, and numerical integration.
Download: mymath.tgz
mymol: Contains classes to deal with atoms, molecules, lattices, and various molecule file formats (xyz, pdb, psf, dcd, and mol2).
Download: mymol.tgz
crystdist: Contains classes to do positional and orientational statistics on molecular geometries, and to calculate crystal order parameters.
Download: crystdist.tgz
getpeaks: A utility to find peaks in the distribution function of distances, bond orientations, relative orientations and internal degrees of freedom for a given geometry.
Download: getpeaks.tgz
cryststat: A utility to find averages and concentration parameters for a model of the pair distribution function of distances, bond orientations, relative orientations and internal degrees of freedom given a reference set of peaks (from getpeaks) and a molecular dynamics trajectory.
Download: cryststat.tgz
copcalc: A utility to calculate crystal order parameters for a given geometry.
Download: copcalc.tgz
cop2pdb: A visualization tool for crystal order parameters.
Download: cop2pdb.tgz
pkt2pdb: A visualization tool for the pair distribution function obtained by getpeaks.
Download: pkt2pdb.tgz
smcv: Contains classes to use the string method in collective variables using crystal order parameters.
Download: smcv.tgz
restforce: A utility to calculate the average restraint forces from a restrained molecular dynamics simulation using crystal order parameters.
Download: restforce.tgz
smcvstep: A utility to carry out steps of the string method in collective variables. Originally written to work with crystal order parameters, but can be easily modified to use any set of order parameters by changing the definition of the class opdfile (see smcv).
Download:
opd2cop: A visualization tool for restraint forces from restrained molecular dynamics simulations using crystal order parameters.
Download: opd2cop.tgz