biod.pnpi.spb.ru
/
alexxy
/
gromacs.git
/ search
commit
grep
author
committer
pickaxe
?
search:
re
summary
|
shortlog
|
log
|
commit
|
commitdiff
|
tree
first ⋅ prev ⋅
next
Remove unused environment variables from docs
2021-01-29
Christian Blau
Update release note on QM/MM deprication
commit
|
commitdiff
|
tree
2021-01-27
Christian Blau
Clarify lambda vector usage with figure in manual
commit
|
commitdiff
|
tree
2021-01-07
Christian Blau
Prepare for GROMACS 2020.6
commit
|
commitdiff
|
tree
2021-01-06
Christian Blau
GROMACS version 2020.5
commit
|
commitdiff
|
tree
2021-01-05
Christian Blau
Fix copyright year
commit
|
commitdiff
|
tree
2020-10-22
Christian Blau
Change outdated remdine references to gitlab
commit
|
commitdiff
|
tree
2020-10-21
Christian Blau
Ensure that gmx covar does not access indices out of...
commit
|
commitdiff
|
tree
2020-10-21
Christian Blau
Clarify that mdtutorials are not provided by the gromacs...
commit
|
commitdiff
|
tree
2020-10-13
Christian Blau
Add missing header in shake to fix mac clang compilation
commit
|
commitdiff
|
tree
2020-10-09
Christian Blau
Remove dysfunctional QMMM interface pt5
commit
|
commitdiff
|
tree
2020-10-02
Christian Blau
Fix FEP lambda interpolation for reruns
commit
|
commitdiff
|
tree
2020-10-01
Christian Blau
Fix the FEP lambda interpolation
commit
|
commitdiff
|
tree
2020-09-22
Christian Blau
Nelder-Mead downhill simplex optimisation
commit
|
commitdiff
|
tree
2020-09-16
Christian Blau
Extend user docs on affine transformations for densities
commit
|
commitdiff
|
tree
2020-09-15
Christian Blau
All coordinates in the density-guided-simulation group...
commit
|
commitdiff
|
tree
2020-09-10
Christian Blau
Simplify and fix how lambda values are set
commit
|
commitdiff
|
tree
2020-09-08
Christian Blau
Allow density-guided simulations to translate structure
commit
|
commitdiff
|
tree
2020-09-07
Christian Blau
Fix clang-format failure in coordinatetransformation.h
commit
|
commitdiff
|
tree
2020-09-07
Christian Blau
Implement affine coordinate transformation
commit
|
commitdiff
|
tree
2020-09-04
Christian Blau
String to array conversion functions
commit
|
commitdiff
|
tree
2020-08-13
Christian Blau
Remove superfluous math utility functions
commit
|
commitdiff
|
tree
2020-08-10
Christian Blau
Move density fitting checkpointing into state
commit
|
commitdiff
|
tree
2020-08-07
Christian Blau
Fixed the mis-fix
commit
|
commitdiff
|
tree
2020-07-07
Christian Blau
Move finalising routine into mtop
commit
|
commitdiff
|
tree
2020-07-02
Christian Blau
Coordinate transformation on single RVecs
commit
|
commitdiff
|
tree
2020-07-01
Christian Blau
Updated the change management documentation
commit
|
commitdiff
|
tree
2020-04-17
Christian Blau
proposed fix for redmine bug #3403
commit
|
commitdiff
|
tree
2020-03-16
Christian Blau
Remove dysfunctional QMMM interface pt4
commit
|
commitdiff
|
tree
2020-03-16
Christian Blau
Remove dysfunctional QMMM interface pt3
commit
|
commitdiff
|
tree
2020-03-16
Christian Blau
Remove dysfunctional QMMM interface pt2
commit
|
commitdiff
|
tree
2020-03-16
Christian Blau
Remove dysfunctional QMMM interface pt1
commit
|
commitdiff
|
tree
2020-03-11
Christian Blau
Amend optional documentation
commit
|
commitdiff
|
tree
2020-03-05
Christian Blau
Add function calls to MdModules to sign up for notifications
commit
|
commitdiff
|
tree
2020-03-05
Christian Blau
Split off implementation details of MdModuleNotification
commit
|
commitdiff
|
tree
2020-03-04
Christian Blau
Save excluded non-bonded interactions in .tpr file
commit
|
commitdiff
|
tree
2020-03-04
Christian Blau
Add classhelper macro to forbid copy, move and any...
commit
|
commitdiff
|
tree
2020-02-25
Christian Blau
Document density-fit cross-correlation in .mdp options
commit
|
commitdiff
|
tree
2020-02-18
Christian Blau
Split MdModuleNotifications into topics
commit
|
commitdiff
|
tree
2020-02-12
Christian Blau
Introduce readXvgData to read xvg data into std::vector
commit
|
commitdiff
|
tree
2020-01-31
Christian Blau
Documentation fix for local atom set data
commit
|
commitdiff
|
tree
2019-12-20
Christian Blau
Remove problematic output of gmx angle
commit
|
commitdiff
|
tree
2019-12-15
Christian Blau
Fix densityfitting stalling and energies
commit
|
commitdiff
|
tree
2019-12-12
Christian Blau
Densityfitting - enforce similarity increase with adaptive...
commit
|
commitdiff
|
tree
2019-12-06
Christian Blau
Change arbitrary units to counts in RMSD distance distributi...
commit
|
commitdiff
|
tree
2019-12-05
Christian Blau
Relax cross-correlation test precision
commit
|
commitdiff
|
tree
2019-12-04
Christian Blau
Remove cutoff-scheme group from default mdout.mdp output
commit
|
commitdiff
|
tree
2019-12-02
Christian Blau
Relax test tolerance for cross correlation measure...
commit
|
commitdiff
|
tree
2019-11-28
Christian Blau
Fix check-pointing for density guided simulations
commit
|
commitdiff
|
tree
2019-11-25
Christian Blau
Fix duplicate CONNECT records in pdb files
commit
|
commitdiff
|
tree
2019-11-25
Christian Blau
Read mrc density map format with all endianesses.
commit
|
commitdiff
|
tree
2019-11-25
Christian Blau
Check mrc header for sanity
commit
|
commitdiff
|
tree
2019-11-24
Christian Blau
InMemorySerializer with endianess swap.
commit
|
commitdiff
|
tree
2019-11-07
Christian Blau
Stochastic dynamics - document that nsttcouple is ignored
commit
|
commitdiff
|
tree
2019-11-01
Christian Blau
Fix cross-correlation calculation instability
commit
|
commitdiff
|
tree
2019-10-22
Christian Blau
Fix nst in density-fitting module
commit
|
commitdiff
|
tree
2019-10-18
Christian Blau
Manual entry and .mdp option for adaptive force scaling
commit
|
commitdiff
|
tree
2019-10-18
Christian Blau
genion: prohibit ion placement close to non-solvent
commit
|
commitdiff
|
tree
2019-10-18
Christian Blau
Basic refactoring genion and adding test
commit
|
commitdiff
|
tree
2019-10-18
Christian Blau
Adaptive force scaling for densityfitting
commit
|
commitdiff
|
tree
2019-10-16
Christian Blau
Exponential moving average
commit
|
commitdiff
|
tree
2019-09-23
Christian Blau
Grompp error for mismatching nst for energy calulation...
commit
|
commitdiff
|
tree
2019-09-23
Christian Blau
Amendments to density fitting manual section
commit
|
commitdiff
|
tree
2019-09-22
Christian Blau
Add cross-correlation as density simlarity measure
commit
|
commitdiff
|
tree
2019-09-19
Christian Blau
Check input record also in tests
commit
|
commitdiff
|
tree
2019-09-19
Christian Blau
Consistently change densityfitting spreading weight...
commit
|
commitdiff
|
tree
2019-09-18
Christian Blau
Add mdp option documentation for density fitting.
commit
|
commitdiff
|
tree
2019-09-12
Christian Blau
Manual entry for density guided simulations
commit
|
commitdiff
|
tree
2019-09-12
Christian Blau
Add release note for density fitting.
commit
|
commitdiff
|
tree
2019-09-11
Christian Blau
Add comments to grompp generated .mdp output for densityfitting
commit
|
commitdiff
|
tree
2019-09-11
Christian Blau
End to end test for density fitting
commit
|
commitdiff
|
tree
2019-09-11
Christian Blau
Densityfitting write int64_t indices instead of gmx...
commit
|
commitdiff
|
tree
2019-09-10
Christian Blau
Use the current mass instead of massA in density fitting...
commit
|
commitdiff
|
tree
2019-09-10
Christian Blau
Account for reference density origin shift in pbc correction
commit
|
commitdiff
|
tree
2019-09-09
Christian Blau
Relative entropy as density similarity measure
commit
|
commitdiff
|
tree
2019-09-09
Christian Blau
Add option to normalize densities prior to density...
commit
|
commitdiff
|
tree
2019-09-09
Christian Blau
Adding every N-steps option to densityfitting
commit
|
commitdiff
|
tree
2019-09-06
Christian Blau
Adding energy output field for density fitting
commit
|
commitdiff
|
tree
2019-09-06
Christian Blau
Periodic boundary correction for density fitting
commit
|
commitdiff
|
tree
2019-09-05
Christian Blau
Add reference density file option to densityfitting
commit
|
commitdiff
|
tree
2019-09-04
Christian Blau
Fix double overload in LocalAtomSet code when gmx:...
commit
|
commitdiff
|
tree
2019-09-04
Christian Blau
Read mrc file using file name
commit
|
commitdiff
|
tree
2019-09-01
Christian Blau
Add checkpointing for MdModules
commit
|
commitdiff
|
tree
2019-08-30
Christian Blau
Constructing local atom sets for density fitting
commit
|
commitdiff
|
tree
2019-08-30
Christian Blau
LocalAtomSet construction with vectors of gmx::index
commit
|
commitdiff
|
tree
2019-08-30
Christian Blau
Implementing the density fitting force provider
commit
|
commitdiff
|
tree
2019-08-27
Christian Blau
Add density fitting parameters
commit
|
commitdiff
|
tree
2019-08-27
Christian Blau
Access to GaussTransform3D data
commit
|
commitdiff
|
tree
2019-08-27
Christian Blau
Add index group option to density fitting
commit
|
commitdiff
|
tree
2019-08-26
Christian Blau
Activation of density fitting and move of module notifications
commit
|
commitdiff
|
tree
2019-08-25
Christian Blau
Index groups for MdModules from grompp
commit
|
commitdiff
|
tree
2019-08-17
Christian Blau
Fix segfault with old tprs processing internal parameters
commit
|
commitdiff
|
tree
2019-08-15
Christian Blau
Move densityfitting options and output into seperate...
commit
|
commitdiff
|
tree
2019-08-14
Christian Blau
Info class to name and generate the densityfitting...
commit
|
commitdiff
|
tree
2019-08-14
Christian Blau
Internal parameter storage for IMDModules
commit
|
commitdiff
|
tree
2019-08-08
Christian Blau
Harmonize mrc density format extents with rest of code.
commit
|
commitdiff
|
tree
2019-08-08
Christian Blau
Provide callbacks/notifications for MDModules
commit
|
commitdiff
|
tree
2019-07-26
Christian Blau
Fix failing check-source target on python3.6
commit
|
commitdiff
|
tree
2019-07-24
Christian Blau
Fix HTML source documenation error caused by GaussTransform3D
commit
|
commitdiff
|
tree
2019-06-28
Christian Blau
Add copy and move operations to density similarity
commit
|
commitdiff
|
tree
2019-06-28
Christian Blau
Add class to look up density fitting amplitudes
commit
|
commitdiff
|
tree
next