Plumed
PLUMED (PLUgin for MolEcular Dynamics) is an open-source, community-developed library that provides a wide range of different methods for enhanced sampling in molecular dynamics. It can be used with several MD codes.
Available
- Puhti: 2.7.4, 2.8.0
- Mahti: 2.6.3, 2.7.2
- LUMI: 2.8.2
License
The PLUMED license (L-GPL) also allows it to be interfaced with proprietary software.
Usage
The standalone module of plumed is for building your own applications and linking with
plumed, or analysing results performed with such code. To use, first give module spider
to locate all versions and their library dependencies:
module spider plumed
module load <dependencies reported by the spider command> plumed/<version>
On LUMI, you need to first load the CSC module tree into use with module use /appl/local/csc/modulefiles.
If you want to run molecular dynamics with plumed, either compile your MD engine of choice with plumed (see selection e.g. here), or use e.g. Gromacs, which is available at CSC.
References
Cite your work with Plumed with:
This work was carried out using the open-source, community-developed PLUMED library
[1], version 2.x [2] (or alternatively version 1.x [3]).
[1] The PLUMED consortium. Promoting transparency and reproducibility in enhanced molecular simulations, Nat. Methods 16, 670 (2019)
[2] G.A. Tribello, M. Bonomi, D. Branduardi, C. Camilloni, G. Bussi. PLUMED2: New feathers for an old bird, Comp. Phys. Comm. 185, 604 (2014), preprint available as arXiv:1310.0980
[3] M. Bonomi, D. Branduardi, G. Bussi, C. Camilloni, D. Provasi, P. Raiteri, D. Donadio, F. Marinelli, F. Pietrucci, R.A. Broglia and M. Parrinello. PLUMED: a portable plugin for free energy calculations with molecular dynamics, Comp. Phys. Comm. 180, 1961 (2009), preprint available as arXiv:0902.0874