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Jan 2023 Collective variable derived from AlphaFold Use AlphaFold output as collective variable as describe in our article. Jan 2023 Metadynminer and Metadynminer3D Article on Metadynminer and Metadynminer3D is out in R Journal. Feb 2022 Metadynminer Masterclass Metadynminer was a part of Plumed Masterclass 2022. Check our tutorial and Youtube videos from the introduction and task solution. Jan 2022 Property map force field correction Correction of force field by ORCA + Plumed, see our article in J. Chem. Inf. Model.. Oct 2020 Metadynminer preprint Check our prepirnt on Metadynminer R package for analysis of the results of metadynamics in Plumed Oct 2020 Metadynminer3D Version of Metadynminer for visualization of 3D free energy surfaces is available. Check Metadynminer3D. Jul 2020 Time-lagged t-SNE If you use t-SNE to analyse molecular simulation trajectories try our time-lagged version. In contrast to conventional t-SNE it focuses on slow motions and makes it possible to identify kinetic traps. The paper was published on-line: Pavel Kriz and Vojtech Spiwok: Time-Lagged t-Distributed Stochastic Neighbor Embedding (t-SNE) of Molecular Simulation Trajectories. Front. Mol. Biosci. 2020, 7, 132. PDF Apr 2019 anncolvar Try our anncolvar tool for approximation of collective variables by neural networks. The paper was published on-line: Dalibor Trapl, Izabela Horvacanin, Vaclav Mareska, Furkan Ozcelik, Gozde Unal and Vojtech Spiwok: Anncolvar: Approximation of Complex Collective Variables by Artificial Neural Networks for Analysis and Biasing of Molecular Simulations. Front. Mol. Biosci. 2019, 6, 25. PDF Sep 2018 Metadynminer Try our new R package metadynminer for visualisation and analysis of metadynamics results. Jul 2018 Add your HILLS file to metadyn.vscht.cz We have enabled users to share their HILLS files on metadyn.vscht.cz. You need to register at http://metadyn.vscht.cz/?q=user. After being approved by metadyn.vscht.cz staff you can login and fill the form at http://metadyn.vscht.cz/?q=addhills. MetadynView can be launched by clicking to a link. You can share your HILLS file on Facebook, Twitter and other networks. Mar 2018 Best poster award for Zoran Sucur from XV Discussions in Structural Molecular Biology and 2nd User Meeting of CIISB in Nove Hrady, congratulations! Dec 2017 Merry Christmas and Happy New Year 2018: http://metadyn.vscht.cz/?q=node/12 Nov 2017 Try syntax highlights for Plumed files in Midnight Commander: https://github.com/spiwokv/mc_syntax_for_Plumed Oct 2017 We have shown that Flying Gaussian and free energy surface reweighting can work together. See proof in the article P. Křìž, Z. Šućur & V. Spiwok: Free Energy Surface Prediction by Flying Gaussian Method: Multi-System Representation. Journal of Physical Chemistry B accepted (2017) http://dx.doi.org/10.1021/acs.jpcb.7b09337. Aug 2017 Flying Gaussian Plumed can be found at https://github.com/spiwokv/plumed2 May 2017 See you at PLUMED Tutorial and User Meeting April 2017 At https://github.com/spiwokv/FlyingGaussianTutorial you can find a flying Gaussian tutorial. April 2017 Well-tempered version of Altruistic metadynamics was published. Well-tempered MPI-based Altruistic metadynamics Plumed hack can be found here: MetaD.cpp. Compile with Plumed 2.2.0 and use with WALKERS_MPI ALTFACTOR=0.5 ALTTYPE=4. The parameter ALTFACTOR controls the the factor α, i.e. the "degree of altruism". Higher bias factor values must be used compared with conventional well-tempered metadynamics (typically the value of conventional bias factor multiplied by the number of walkers). ALTTYPE=4 means that for two walkers and HEIGHT=1.0 a hill of height 1.5 is added to "own" system and 0.5 to the other system. ALTTYPE=3 means that for two walkers and HEIGHT=1.0 a hill of height 1.0 is added to "own" system and 0.333333 to the other system. ALTTYPE=2 and ALTTYPE=1 are experimental. April 2017 New Metadyn View facelift. March 2017 Close structure algorthm for fast (R)MSD calculation in path and property map CVs was published together with Jana Pazurikova, Maria Simkova and Ales Krenek. We are working on implementation to the official Plumed. December 2016 New version of Metadyn View and revised web site is provided at metadyn.vscht.cz. November 2016 Flying Gaussian Plumed hack can be found here: MetaD.cpp. Compile with Plumed 2.2.0 and use with PACE=1 WALKERS_MPI FLYING_GAUSSIAN. PACE controls the rate of hill moves (PACE=1 means move in every step). Free energy surface can be obtained from the COLVAR file. September 2016 Our new "Flying Gaussian" sampling enhancment method has been published in JCTC. Flying Gaussian uses multiple walkers similarly to multiple walker metadynamics. Each walker is associated with one Gaussian bias potential hill, which moves together with CV evolution. When multiple walkers accumulate in one minimum they are repulsed by their Gaussians. May 2016 Try our Gibbs energy - equilibrium constant and Eyring equation online calculator. April 2016 New video demonstrating altruistic metadynamics is available at Youtube. March 2016 We would apreciate any feedback regarding our metadynamics viewer MetadynView. Please find few minutes to fill a questionaire. February 2016 We have published a study presenting altruistic metadynamics. This variant of multiple walker metadynamics makes it possible to simulate chemically different systems and to predict their free energy surfaces. You can add this MetaD.cpp file to Plumed 2.2 and compile. Altruistic metadynamics can be used as a multiple walker metadynamics with WALKERS_MPI=off (WALKERS_MPI=on in progress) and with ALTFACTOR=0-1.