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Commits : Listings

Analyzed 12 months ago. based on code collected 12 months ago.
Jan 20, 2023 — Jan 20, 2024
Commit Message Contributor Files Modified Lines Added Lines Removed Code Location Date
fixes to the modified tRNA parameters and biotypes in examples/amoebabio09_trna.prm
Michael J. Schnieders
More... over 14 years ago
add RefinementMinimize class; b factor and joint coordinate and bfactor refinement support
Tim Fenn
as fenn
More... over 14 years ago
added fallback scaling for the LBFGS minimizer
Michael J. Schnieders
as schnied
More... over 14 years ago
first refinement script
Michael J. Schnieders
More... over 14 years ago
Merge branch 'master' of ssh://git.kenai.com/ffx~source
Michael J. Schnieders
More... over 14 years ago
Minor changes to RefinementEnergy
Michael J. Schnieders
More... over 14 years ago
initial XRayEnergy class; add functions for updating coordinates for refinement
Tim Fenn
as fenn
More... over 14 years ago
Merge branch 'master' of ssh://git.kenai.com/ffx~source
Michael J. Schnieders
More... over 14 years ago
updated bonded energy terms to make TINKER and FFX consistent for modified RNA residues of PHE-tRNA
Michael J. Schnieders
More... over 14 years ago
edit FiniteDifferenceTest
Tim Fenn
as fenn
More... over 14 years ago
revert to previous bulk solvent model; dynamically assign grid radius in CrystalReciprocalSpace; minor speedups in CrystalReciprocalSpace; assign and use form factor indexes where possible
Tim Fenn
as fenn
More... over 14 years ago
Fixed null pointer exception in PDBFilter, updated to AppleJavaExtensions v. 1.4
Michael J. Schnieders
More... over 14 years ago
removed s24/java/14/classes/ffx/numerics/fft/Complex3DCuda.class
Michael J. Schnieders
More... over 14 years ago
Merge branch 'master' of ssh://git.kenai.com/ffx~source
Michael J. Schnieders
More... over 14 years ago
added 1EHZ and 4TNA structures and reflections, added a preliminary AMOEBA force field for modified RNAs
Michael J. Schnieders
More... over 14 years ago
added automatic atom typing for modified RNAs 2MG, H2U, M2G, OMC, OMG, YYG, PSU, 5MC, 7MG, 5MU and 1MA
Michael J. Schnieders
More... over 14 years ago
merge with upstream; initial merge of crystalreciprocalspace objects (new bulk solvent model method); using VDW radius in bulk solvent
Tim Fenn
as fenn
More... over 14 years ago
printed temperature and kinetic energy are computed prior to full-step velocity modifications by the thermostat
Michael J. Schnieders
More... over 14 years ago
fixed a bug in the torque method, fixed the alternate conformers code, replaced StringBuffer with non-synchornized StringBuilder
Michael J. Schnieders
More... over 14 years ago
added a default Adiabtic thermostat, testgrad script, persistent Random number generator for the Bussi thermostat, and minor tweaks throughout MolecularDynamics to require use of a thermostat - ie. Adibatic should be used for no coupling to an external bath
Michael J. Schnieders
More... over 14 years ago
fixed a small bug in the new SpatialDensitySchedule for the final chunk range
Michael J. Schnieders
More... over 14 years ago
created a new schedular for the SpatialDensity parallelization, added Zn+2 parameters to
Michael J. Schnieders
More... over 14 years ago
Now grid chunks per CPU correspond to non-empty chunks
Michael J. Schnieders
More... over 14 years ago
minor tweak to SpatialDensityRegion
Michael J. Schnieders
More... over 14 years ago
Merge branch 'master' of ssh://git.kenai.com/ffx~source
Michael J. Schnieders
More... over 14 years ago
PotentialEnergy instance is now created after a system is read in, SpatiaSpatialDensity parallelization was modified to explicity include only work chunks that have atoms assigned to them
Michael J. Schnieders
More... over 14 years ago
faithful reproduction of Jiang and Brunger bulk solvent model
Tim Fenn
as fenn
More... over 14 years ago
fixed a bug in the PDBFilter when reading multiple PDBs into one FFXSystem
Michael J. Schnieders
More... over 14 years ago
Merge branch 'master' of ssh://git.kenai.com/ffx~source
Michael J. Schnieders
More... over 14 years ago
added support for parsing multiple PDB files into the one MolecularAssembly
Michael J. Schnieders
More... over 14 years ago