Application Index

This is a collection of programs for performing Monte Carlo (MC) statistical mechanics simulations.

The gcmc program is used to perform a molecular simulation in the grand canonical ensemble. The program is capable of simulating molecular models composed of Lennard-Jones or Buckingham exponential-6 sites to describe the non-polar forces and point charges to represent the polar forces. Configurational-bias techniques are used to insert molecules. The program is also capable of using early rejection and expanded ensemble techniques to aid in inserting the molecules. Additionally, reservoir techniques are available to create molecules with complex architecture and/or stiff intramolecular potentials. The program is written with the assumption that histogram reweighting techniques will be used to calculate the thermophysical properties. Therefore, the main output of the program is a histogram of the frequency of observing the system with a given particle number and energy. Finally, Hamiltonian scaling techniques are incorporated into the program. This allows multiple potential models to be simulated during the same run.
View Application Entry for gcmc (Grand Canonical Monte Carlo program)

MMC is a Metropolis Monte Carlo program for the simulation of molecular assemblies in the canonical, grand-canonical and isothermal-isobaric ensembles employing several convergence acceleration techniques (e.g., force-biased displacement, preferential selection of solvent to be moved, cavity-biased insertion, virial-biased volume change). The simulated system generally consists of one part called solute and a collection of identical rigid molecules called solvent. The solute can consist of any number of molecules that can move freely and have any or all of their torsional degrees of freedom sampled. Bond lengths and bond angles are kept fixed. Solvation free-energy (change) can be calculated using thermodynamic integration, the perturbation formula the overlapo ratio method, the (cavity) Widom insertion method or by potential of mean force calculation using the adaptive umbrella sampling method. Both continuous deformation and creation/annihilation paths can be used. The solute environment can be analyzed based on the Proximity Criterion and the resulting analysis can be visualized by color coding the solute atoms based on selected analysis result. The Proximity Analysis can be also performed on Charmm or Amber trajectories. The calculations can use Charmm, Amber, Gromos, OPLS, EPEN and Clementi potentials. Many atomtypes are built in, additional ones can be defined by the user.
View Application Entry for MMC (Metropolis Monte Carlo program)

The BOSS program performs (a) Monte Carlo (MC) statistical mechanics simulations for solutes in a periodic solvent box, in a solvent cluster, or in a dielectric continuum including the gas phase, and (b) standard energy minimizations, normal mode analysis, and conformational searching. The energetics are represented with the OPLS force fields or the AM1 or PM3 semiempirical MO methods. Besides the quantitative structural and energetic results, other quantities are computed including dipole moments and solvent accessible surface areas that are valuable for many applications such as structure-activity relations.
View Application Entry for BOSS

MCPRO is a program which performs Monte Carlo statistical mechanics simulations of peptides, proteins, and nucleic acids in solution; it was derived from BOSS, but makes extensive use of the concept of residues. It does not include conformational search, quantum mechanics, or normal mode calculations. The MC simulations can be performed in a periodic solvent box, in a solvent cluster, or in a dielectric continuum including the gas phase. Energy minimizations can also be performed with several optimizers including conjugate gradient. NMR constraints (NOE and torsion angle) can be added for NMR structure refinements via simulated annealing. Free energy changes can be computed via FEP calculations and have been used extensively for studying protein-ligand binding. Input files are provided for ca. 1000 common organic molecules and drugs. Output inlcudes molecular structures in PDB or mol format for easy display with standard graphics programs including XChemEdit.
View Application Entry for MCPRO

ARTwork is a program for molecular dynamics and Monte Carlo simulations based on Effective Medium Theory.
View Application Entry for ARTwork

Configurational Bias Monte Carlo (CBMC) is a recent technique to compute thermodynamic properties of flexible molecules. It has been used to study the adsorption behavior of linear and branched alkanes in zeolites and the vapour-liquid equilibrium of linear and branched alkanes.
View Application Entry for CBMC (Configurational Bias Monte Carlo)