67 citations · 93 across the 6 of their papers we have counts for
7 papers
MD-LLM-2: A Transferable Language Model of Molecular Dynamics with Physical Conditioning and Explicit Path Probabilities
Mhd Hussein Murtada, Z. Faidon Brotzakis, Michele Vendruscolo
Molecular dynamics (MD) simulations model the motion of proteins between conformational states, but crossing free energy barriers and sampling multiple thermodynamic conditions rem…
MD-LLM-1: A Large Language Model for Molecular Dynamics
Mhd Hussein Murtada, Z. Faidon Brotzakis, Michele Vendruscolo
Molecular dynamics (MD) is a powerful approach for modelling molecular systems, but it remains computationally intensive on spatial and time scales of many macromolecular systems o…
PLUMED Tutorials: a collaborative, community-driven learning ecosystem
Gareth A. Tribello, Massimiliano Bonomi, Giovanni Bussi +60
In computational physics, chemistry, and biology, the implementation of new techniques in a shared and open source software lowers barriers to entry and promotes rapid scientific p…
Force field optimization by imposing kinetic constraints with path reweighting
P. G. Bolhuis, Z. F. Brotzakis, B. G. Keller
Empirical force fields employed in molecular dynamics simulations of complex systems can be optimised to reproduce experimentally determined structural and thermodynamic properties…
A method of incorporating rate constants as kinetic constraints in molecular dynamics simulations
Z. Faidon Brotzakis, Michele Vendruscolo, Peter. G. Bolhuis
From the point of view of statistical mechanics, a full characterisation of a molecular system requires the experimental determination of its possible states, their populations and…
Folding a Small Protein Using Harmonic Linear Discriminant Analysis
Dan Mendels, Giovannimaria Piccini, Z. Faidon Brotzakis +2
Many processes of scientific importance are characterized by time scales that extend far beyond the reach of standard simulation techniques. To circumvent this impediment a plethor…
Bayesian Calibration of Force-fields from Experimental Data: TIP4P Water
Ritabrata Dutta, Zacharias Faidon Brotzakis, Antonietta Mira
Molecular dynamics (MD) simulations give access to equilibrium structures and dynamic properties given an ergodic sampling and an accurate force-field. The force-field parameters a…