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Protocols

PLUMED specifications

Information


Unique identifier OMICS_25251
Name PLUMED
Alternative name PLUMED2
Software type Framework/Library, Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C++, Fortran, Shell (Bash)
Parallelization MPI
License GNU Lesser General Public License version 3.0
Computer skills Advanced
Version 2.4.0
Stability Stable
Requirements
GNU make, C++ compiler, patch, dirent.h, xxd
Maintained Yes

Download


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Versioning


No version available

Documentation


Maintainers


  • person_outline Giovanni Bussi
  • person_outline Massimiliano Bonomi
  • person_outline Gareth Tribello
  • person_outline Carlo Camilloni
  • person_outline Davide Branduardi

Additional information


https://plumed.github.io/doc-v2.3/user-doc/html/index.html

Publications for PLUMED

PLUMED citations

 (43)
library_books

Structural insights into positive and negative allosteric regulation of a G protein coupled receptor through protein lipid interactions

2018
Sci Rep
PMCID: 5849739
PMID: 29535353
DOI: 10.1038/s41598-018-22735-6

[…] haracteristics and protein-membrane interactions: i) the distance(s) between ionic-lock residue R1313.50 (terminal nitrogen atoms) and closest lipid phosphate group (centre-of-mass) was measured with PLUMED; (ii) membrane thickness calculated as average distance from lower to upper-leaflet phosphorus atoms, implementing default settings of MEMBPLUGIN within VMD over total simulation time; (iii) me […]

call_split

Molecular basis for potentiation of Cx36 gap junction channel conductance by n alcohols and general anesthetics

2018
Biosci Rep
PMCID: 5803492
PMID: 29298877
DOI: 10.1042/BSR20171323
call_split See protocol

[…] All molecular dynamics (MD) calculations were performed with the GROMACS (Groningen Machine for Chemical Simulations, version 2016.2) []. Time steps of 2-fs duration were used for all MD simulations. PLUMED (version 2.3.0) [] was used for steered MD (SMD). We used the Amber99 SB-ILDN [] force field for the protein and the SPCE [] for all water molecules of the system. The electroneutrality of the […]

call_split

Predicting peak spectral sensitivities of vertebrate cone visual pigments using atomistic molecular simulations

2018
PLoS Comput Biol
PMCID: 5798944
PMID: 29364888
DOI: 10.1371/journal.pcbi.1005974
call_split See protocol

[…] harmm-gui.org) web server. Molecular dynamics (MD) simulations were carried out using GROMACS v5.1.2 []. Analysis of the internal degrees of freedom i.e. torsion and bond angles was carried out using plumed-driver tool from PLUMED v2.2. []. Molecular visualization of MD simulations was done in VMD []. […]

library_books

RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview

2018
PMCID: 5920944
PMID: 29297679
DOI: 10.1021/acs.chemrev.7b00427

[…] procedure (see ).Easy-to-detect unstable behavior of metadynamics when the chosen CVs are not sufficient is perhaps one reason why the community using this method has developed a large number of CVs. PLUMED, and colvars are software plugins that implement a very large number of possible CVs and can be used both with metadynamics and with other CV-based enhanced sampling methods. Having a large dat […]

library_books

Sequence dependent response of DNA to torsional stress: a potential biological regulation mechanism

2017
Nucleic Acids Res
PMCID: 5829783
PMID: 29267977
DOI: 10.1093/nar/gkx1270

[…] mational analysis methodology (), which controls the total helical twist between two chosen base pairs, allowing both under- and overtwisting to be imposed. This restraint has been implemented within PLUMED free energy library () and can thus be used in conjunction with a variety of standard all-atom MD software packages. While determining the total twist of a chosen segment of DNA, our restraint […]

library_books

In silico direct folding of thrombin binding aptamer G quadruplex at all atom level

2017
Nucleic Acids Res
PMCID: 5728390
PMID: 29112755
DOI: 10.1093/nar/gkx1079

[…] l PTMetaD simulations were run for 10–12 μs (per replica) starting from completely unfolded states (). All simulations are were performed using the GROMACS program (5.0.7 version) () patched with the PLUMED 2.3 software (). […]

Citations

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PLUMED institution(s)
Department of Chemistry, University of Cambridge, Cambridge, UK; Department of Chemistry and Institute for Advanced Study, Technische Universität München, Garching, Germany; Dipartimento di Bioscienze, Università degli Studi di Milano, Milan, Italy
PLUMED funding source(s)
Supported by the Technische Universität München – Institute for Advanced Study.

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