Scientific software

Swan

Swan is a small tool that aids the reversible conversion of existing CUDA codebases to OpenCL. Go to Swan

ACEMD

ACEMD is a production bio-molecular dynamics software specially optimized to run on graphics processing units (GPUs) on NVIDIA graphics cards. It reads CHARMM/NAMD and AMBER input files with a simple and powerful configuration interface. ACEMD allows performance equivalent to over 100 CPUs and microsecond long trajectories on workstation hardware. Go to ACEMD

MyDPD

MyDPD is a mesodynamics code in three spatial dimensions, where DPD stands for dissipative particle dynamics. This code is simple but functional. It contains two integrators for the DPD stochastic equations, a simple DPD velocity Verlet and the stochastic Trotter integrators.

Remote Boinc

RBoinc is the scientist-side component of BOINC. It allows researchers to submit, retrieve and manage jobs remotely. See also doi:10.1016/j.cpc.2010.04.007 and http://boinc.berkeley.edu/trac/wiki/RemoteJob.

Utilities

Plumed-GUI: a collective variable analysis tool

The PLUMED collective variable analysis tool VMD plugin provides convenient access to the extensive set of collective variables (CV) defined in the PLUMED software. It allows the use of PLUMED syntax to conduct analysis on MD trajectories, and a convenient interface to prepare the metadynamics CV definitions.

Native contacts plugin

RMSD trajectory tool enhanced with native contacts enables VMD to compute the number of native contacts in a trajectory. It is an extension of the RMSD Trajectory Tool, of which it shares the interface.

Density Profile Tool

The Density Profile Tool is an analysis plugin for VMD that computes 1-D projections of the following atomic density profiles: atomic, mass, charge and electrons.

Diffusion Coefficient Tool

The Diffusion Coefficient Tool is an analysis plugin for VMD that computes one, two or three-dimensional diffusion coefficients during a loaded trajectory based on average mean square displacements.

VMD extension functions

VMD extension functions is a collection of TCL-VMD functions and iterators that support extraction of structural data from large-scale simulations. They provide simple semantics to iterate a block of code over frames or trajectory files, functions to compute the number of native contacts, distance matrices, and more.

Cast structure tool

The Cast structure tool is a modeling plugin which copies the coordinates of a selection A from another selection B, preserving A's topology. Coordinates of A's atoms will be copied verbatim when an unambiguous match exists in B; otherwise, the new coordinates will be guessed with a local fit.

Protocols

See the ACEMDtk series of protocol sheets.

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