Skip to content

Latest commit

 

History

History
40 lines (27 loc) · 1.73 KB

README.md

File metadata and controls

40 lines (27 loc) · 1.73 KB
Raw

When using the Dashboard, please cite the reference article:

J. Hénin, Laura J. S. Lopes, G. Fiorin, Human learning for molecular simulations: the Collective Variables Dashboard in VMD, J. Chem. Theo. Comput., 2022, 18, 3, 1945–1956 (https://pubs.acs.org/doi/10.1021/acs.jctc.1c01081).

How to use the Colvars Dashboard in VMD

Using the version included with VMD 1.9.4 alpha or later

Open the graphical interface by clicking the Extensions/Analysis/Colvars Dashboard menu item, or by typing cv_dashboard in the VMD terminal.

Complete documentation is available here: http://colvars.github.io/colvars-refman-vmd/colvars-refman-vmd.html#sec:dashboard

Updating the Dashboard manually

The plugin can be updated manually to access recent features that are not yet included in official releases of VMD.

Using VMD 1.9.3 (released in 2016) is not recommended. as of 2021, VMD 1.9.4 "alpha" releases are the de facto current versions.

First, download the Colvars tree from https://github.com/Colvars/colvars/archive/master.zip or clone the git repository. Navigate to the vmd/cv_dashboard subdirectory.

On a Unix-like system with GNU make

Edit the DESTINATION variable in Makefile.local with the path where VMD is installed, and run make -f Makefile.local install (Makefile is used within the VMD plugin distribution, by VMD's own build script, which is why we use Makefile.local). Then start VMD and open the interface using Extensions/Analysis/Colvars Dashboard.

On Windows or if GNU make is not available

Find the path where VMD is installed (by default: C:\Program Files\University of Illinois\VMD) and replace the contents of plugins/noarch/tcl/cv_dashboard1.x with those of vmd/cv_dashboard from the Colvars tree.