Citation

In any publication of scientific results based in part or completely on the use of EMC, please include this reference:

    P.J. in 't Veld and G.C. Rutledge, Macromolecules 2003, 36, 7358

Optionally, a mention of this website can be made. A mailing list for all your questions regarding EMC has been set up at http://matsci.org/emc

Version 9.4.4 (August 1, 2024)

2024-10-06: new upload for all targets fixing issues with CFF force fields.

Switch to an updated version 9.4.4 with corrections in comparison to the August 1, 2023 version (see History).  This version was compiled for MacOS 12.5, Linux (x86_64 and aarch64, 64 bit), and Windows (win32, 64 bit).  All versions have been statically compiled.  Main updates include further generalization of CHARMM and TraPPE force fields. Issues as reported http://matsci.org/emc have been addressed. Please report further issues at this website.

    EMC Setup underwent a major update by modularization of its components and is now available under emc.pl v5.1. The old emc_setup.pl v4.1.5 is still available, but will be phased out with the next online update.

    An updated version of a GUI for use with VMD has been included.  This GUI allows for use of the essential functionality of EMC and is integrated into the VMD framework. The VMD EMC GUI has been updated to run more stable in general and specifically run correctly under Windows.  The VMD plug-in can be found in the ./vmd subdirectory.

    EMC Setup environment mode has been further developed to cover a wider array of options.  Currently supported queueing systems include PBS, LSF, and Slurm.  The latter, however, has been tested the least.  Please adapt ./scripts/run.sh to allow for correct queueing system handling.

    Environments allow for capturing multiple conditions into one setup script, thus functioning as a workflow engine.  EMC setup uses a directory structure to reflect this environment, organizing Bash scripts into build, run, and analyze directories.  Bash scripts serve as wrap-around scripts for EMC setup chemistry scripts, which themselves are a wrap around for creating EMC and LAMMPS input scripts.

    This update allows for definition of multiphase systems, systems including surfaces, and polymers with or without mass distributions.  Examples illustrating new capabilities have been added under ./example/setup for both chemistry and environment modes.  Novice users are advised to check out these examples for further edification.  The manual has been updated to reflect these changes and includes some choice examples.  Note, that the created LAMMPS input script is intended for the newest version of LAMMPS (see -communicate and -chunk).  See the project’s history for a more detailed record of changes.

Description

Enhanced Monte Carlo, or EMC for short, provides an environment for creating and manipulating input structures for particle simulations using atomistic  force fields Born, COMPASS, PCFF, CHARMM, OPLS, and TraPPe, which are typed using typing rules.  Supported coarse-grained force fields DPD, Martini, SDK, and colloidal force fields, are not typed by EMC.  To this end, a scripting language manages access to its functionality.  EMC provides manipulation of molecular or coarse-grained structures through SMILES strings, typing these structures - when needed - for selected force fields, and building conformations applying Monte Carlo principles.  EMC provides output ports to LAMMPS, PDB, and XYZ formats.  Several analysis options for analyzing either internal simulations or trajectories include the cavity energetic sizing algorithm (CESA), density, pressure and energy profiles.  The EMC setup script allows for generation of EMC and LAMMPS input in a convenient matter by providing a workflow environment for spawning single or multiple simulations with one script.  Check the ‘Features’ page for a brief overview of EMC features.

    Force field support includes CGENFF and Born force field support.  The latter is used to describe metal oxides.  As of August 19, 2016, ester and imide rules for opls/2012/opls-ua have been corrected.  Bonded contributions have been added to charmm/c36a/cgenff for typing of (poly) propylene oxide.  As of December 20, 2016, internal issues with conversion of OPLS, TraPPE, and GROMACS torsion parameters to LAMMPS multi harmonic representations have been resolved.  Adaptations have been made to OPLS force fields to allow for use of TIP water models.  Minor adaptations have been made to OPLS-UA to correctly represent PET.  Internal issues with conversion of OPLS, TraPPE, and GROMACS torsion parameters to LAMMPS multi harmonic representations have been resolved.  Another addition setup script, which produces EMC build and LAMMPS input scripts.

About this Project

This is the EMC: Enhanced Monte Carlo project ("montecarlo"),

authored by Pieter J. in ’t Veld

This project was registered on SourceForge.net on May 15, 2008, and is described by the project team as follows:

EMC: Enhanced Monte Carlo; A multi-purpose modular and easily extendable solution to molecular and mesoscale simulations