https://github.com/whitead/plumed-experiments

A fork of plumed which has experiment directed metadynamics and experiment directed simulation implementations.
https://github.com/whitead/plumed-experiments

Last synced: about 1 month ago
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A fork of plumed which has experiment directed metadynamics and experiment directed simulation implementations.

• Host: GitHub
• URL: https://github.com/whitead/plumed-experiments
• Owner: whitead
• License: lgpl-3.0
• Created: 2015-07-14T12:35:16.000Z (over 9 years ago)
• Default Branch: v-1.0
• Last Pushed: 2017-07-24T21:02:59.000Z (over 7 years ago)
• Last Synced: 2024-10-16T02:59:08.614Z (3 months ago)
• Language: C
• Size: 3.3 MB
• Stars: 3
• Watchers: 3
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README
  • Changelog: CHANGES
  • License: COPYING

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README

        
PLUMED is a plugin for free-energy calculations in molecular systems which works 

together with some of the most popular molecular dynamics codes, such as 

GROMACS, NAMD, DL_POLY, LAMMPS and the SANDER module in AMBER. It also works with the very fast 

CUDA/GPU MD code ACEMD and, more recently, it has been extended to work with ab initio

 MD codes, such as Quantum-ESPRESSO and CPMD. 

Free-energy calculations can be performed as a function of many order parameters

with a particular focus on biological problems and using state-of-the-art methods 

such as metadynamics, umbrella sampling and Jarzynski-equation based steered MD.

The present software, written in ANSI-C language, can be easily interfaced with

both fortran and C/C++ codes. 

For more information, see:

http://www.plumed-code.org/

If you have any questions, please subscribe to [email protected]

Enjoy!

The PLUMED Developers Team

List of Files:

The most important files that provide the aforementioned functionality are contained in the "common_files" directory:

biasexchange.c  	: enables bias exchange (only GROMACS code) 

dafed.c			: The driven adiabatic free energy (d-AFED) algorithm

hills.c			: calculates the potential energy and the forces coming from Metadynamics 

metadyn.c		: main driver for metadynamics calculation, steered MD and umbrella sampling

metadyn.h		: defines structures, functions and global parameters 

ptmetad.c		: enables metadynamics correction in the MC acceptance of parallel tempering (only GROMACS code) 

read_restraint.c	: main parsing for input file

restraint.c		: calculation of the collective variables implemented 

restraint_*.c		: calculation and reading of the collective variables (see the manual)  

testderivatives.c	: finite difference driver for testing the analytical derivatives of order parameters	

INSTALLATION:

see the INSTALL file in this directory

HOW TO RUN THE TESTS (courtesy of Joost VandeVondele):

see the README file in the tests/ directory