Giacomo Fiorin

icon indicating a website link https://research.ninds.nih.gov/staff-directory/giacomo-fiorin-phd

icon company NIH icon location Bethesda, MD icon location Staff scientist at NIH, studying biological membranes using computational tools

Results 23 issues of Giacomo Fiorin

Bias-exchange metadynamics implementation

This PR contains an implementation of bias-exchange metadynamics (https://doi.org/10.1021/jp067873l) based on the NAMD Tcl scripting interface. Although most of the code is Tcl, the following significant changes are introduced to...

NAMD
script_API

Improve detection of hard/mathematical boundaries

Implements the ability to auto-detect when user-defined boundaries are also "hard" mathematical boundaries. See https://github.com/Colvars/colvars/pull/710#issuecomment-2379363975 Related to #476 and #710

Allowing the script API to return atom IDs even in scalable computations

Issue raised in a conversation a few weeks ago between @HanatoK and Ashkan Fakharzadeh Ghaan at UIUC. Debugging a Colvars configuration in NAMD can be confusing if all the atoms...