NAMD is a molecular dynamics program designed for high-performance simulations of very
large biological objects on CPU-and GPU-based architectures. NAMD offers scalable …

… A sensible approach is to align the two molecules—say, A and B—in their binding poses
and preferentially map each atom in A to an atom in B that is spatially close. This may be …

… B, where B represents a small modification to A), while for virtual screening ABFE accuracy
need only be sufficient to separate binders from nonbinders (a much larger energy separation…

… green solid lines) is performed, followed by a driven nonequilibrium switch (orange dotted
lines), which changes both the configuration and protonation state (arbitrarily labeled A and B)…

This paper presents investigations on the influence of in-situ ionic activation using combination
of three d-metals: Ni, Co and Mo on the hydrogen evolution reaction (HER) mechanism …

… (A) The view of the titanium surface prior to laser action; (B) titanium after 1 laser pulse (B1
the entire spot, B2 the center and B3 the near periphery of the damage area); (C) implant after …

… T) is the unitless scaled free energy profile, (x) is the free energy profile, k B is the … All values
are in units of k B T, except for x̅ α , which is in units of Å. … All values are in units of k B T. …

Enzymes function by stabilizing reaction transition states; therefore, comparison of the
transition states of enzymatic and nonenzymatic model reactions can provide insight into …

… β = 1/k B T, where k B is the Boltzmann constant and T is the temperature. Formally, the
perturbation term, , in eq 1 ought to be replaced by the difference between the reference and the …

Progress in the development of GPU-accelerated free energy simulation software has enabled
practical applications on complex biological systems and fueled efforts to develop more …