METAGUI extends VMD with a graphical user interface that allows constructing a thermodynamic and kinetic model of a given process simulated by long-scale molecular dynamics. METAGUI can analyze both unbiased and metadynamics-based simulations. The structures generated during such a simulation are clustered together into a set of microstates (i.e. structures with similar values of the collective variables) and their relative free energies are then computed by a weighted-histogram procedure.
The most relevant free energy wells are identified by diagonalization of the rate matrix followed by a "smart clustering" analysis in Rodriguez-Laio 2014. This procedure leads to a convenient representation of the metastable states and long-time kinetics of the system which can be compared with experimental data.
The tool allows to seamlessly switch between a collective variables space representation of microstates and their atomic structure representation, which greatly facilitates the set-up and analysis of molecular dynamics trajectories.
METAGUI can read the output of the PLUMED 1.3 and 2.x engines, making it compatible with a number of different molecular dynamics packages like AMBER, NAMD, GROMACS and several others.
Please find the latest release on GitHub at https://github.com/metagui/metagui3.
First, the tool should be installed so that its root directory is
somewhere in TCL's "auto_path". Therefore, either move it into VMD's
plugin directory, or add the following instructions to your .vmdrc
file
lappend auto_path /WHERE/YOU/EXTRACTED/THE/TOOL
vmd_install_extension metagui3 metagui3::metagui "Analysis/Metagui 3.0"
menu main on
Alternatively, you can set TCL's auto path via the TCLLIBPATH
environment variable.
You will also need to compile the FORTRAN code provided in the src
subdirectory (GNU gfortran is recommended): issue
make
in the top directory. This should generate the executable
metagui_util.x. The plugin should automatically detect the location
of the executable. If it doesn't please copy it somewhere in your
PATH, or set the location in the "Advanced settings" tab.
Just source the code as follows
vmd -e run_metagui3.tcl
or, if you want to run from the DEMO_ALA3 directory
TCLLIBPATH=.. vmd -e ../run_metagui3.tcl
See the read me file in that directory.
The METAGUI 3.0 code builds upon METAGUI 2.0, written by Xevi Biarnés, Fabio Pietrucci, Fabrizio Marinelli, Alessandro Laio. Additions were made by Alex Rodriguez, Alessandro Laio and Toni Giorgino.
This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/.
- Includes Paul Walton's scrollable frame code
sframe.tcl, available at http://wiki.tcl.tk/9223 . - Includes the Tablelist 5.15 package, available from http://www.nemethi.de/ .
If you publish results obtained with METAGUI 3, please cite the following paper
Giorgino T, Laio A, Rodriguez A. METAGUI 3: a graphical user interface for choosing the collective variables in molecular dynamics simulations. Computer Physics Communications. https://doi.org/10.1016/j.cpc.2017.04.009
The "smart clustering" algorithm is described in
Rodriguez A, Laio A. Clustering by fast search and find of density peaks. Science. 2014;344(6191):1492-6. http://www.sciencemag.org/content/344/6191/1492.abstract