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VMD
has evolved to version 1.9, featuring
new and improved tools for molecular cell biology.
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Olga Svinarski and VMD
The molecular graphics program
VMD
has evolved to version 1.9, featuring
new and improved tools for molecular cell biology.
A key new tool in VMD permits visual diagnosis of the long-time dynamics
of large structures.
Improved computer power permits now simulation of processes like protein
folding that stretch over microseconds to milliseconds.
While short in human time, the process measured in terms of basic
molecular motion like bond vibration is seemingly endless,
involving hundreds of gigabytes of data and long hours of human attention,
if not automated.
VMD offers now with the
Timeline tool,
a convenient way of scanning such data for key "events" that signal
successful process steps.
Timeline can likewise assist in monitoring the dynamics of large
cellular machines involving millions of atoms.
VMD 1.9 sports other new tools like
ParseFEP
for analyzing so-called free energy perturbation calculations determining
the energy arising in reaction processes as calculated with VMD's sister
program NAMD.
VMD includes now also a lightening fast tool to detect
spatial regularities in the arrangement of small molecules in order to
detect if they constitute disordered or ordered arrangements. By
calculating the so-called
radial distribution function
the tool could
identify plug formation in nanopore sensors due to precipitates that go
undetected by density or visual inspection. Pleasing to the eye, molecular
graphics features in VMD have been enhanced, enabling
faster ray tracing,
new shading features,
X3D
molecular scene export for display in
WebGL-capable
browsers including Chrome, Firefox, and Safari.
See more on the VMD 1.9 release page.