Update behavior for alchemical bonded scaling
[namd.git] / src / Molecule.h
2019-02-01 radakbUpdate behavior for alchemical bonded scaling 34/4934/2
2019-01-11 DavidFix REST2 config parameter name lookup 90/4890/1
2018-08-31 radakbPreliminary implementation of colinear lonepairs 22/4522/4
2018-05-02 Wei JiangREST2 implementation in NAMD 88/3588/10
2018-01-29 radakbFix alchemical coupling + LJcorrection 85/3585/2
2017-12-20 Jim PhillipsFix integer overflows for exclusion counts 56/3456/1
2017-07-17 David HardyMerge "Oops, fix bad path for namdcph.tcl"
2017-07-17 David HardyMerge "Actual example for constant pH using a protein...
2017-07-17 David HardyMerge "Additional example for restarting constant pH"
2017-07-17 David HardyMerge "Initial commit for constant pH (namdcph)"
2017-07-14 melomcrCombined QM/MM updates. 80/2780/6
2017-03-29 Jim PhillipsMinimal change for testing billion-atom systems.
2016-09-29 Jim PhillipsQM/MM interface from Marcelo Melo.
2016-02-07 Jim PhillipsAlchemical features from Brian Radak:
2015-12-29 Jim PhillipsFix ExclusionCheck destructor, etc., as class does...
2015-12-03 Jim PhillipsMake CUDA full exclusion checksum work across multiple...
2013-11-20 Jim PhillipsNew Go GromacsPair implementation from Jonathan Lai.
2013-01-28 Jim PhillipsFrom Lei Huang: Remove possibility for NBTHOLE to alter...
2012-11-27 Jonathan Lai(JLai - 11/27/12)
2012-08-07 Jim PhillipsEnable harmonic constraints for memory optimized builds...
2012-03-08 Chris HarrisonBeginning initial integration of NAMD-OPENATOM QM/MM...
2012-02-21 David Tannerlinear combination of pairwise overlaps (LCPO) for...
2012-02-17 Jim PhillipsGo forces implementation from Jonathan Lai.
2011-12-16 David WellsChanged grid reload code so that it broadcasts complete...
2011-12-02 David WellsAdded Gridforce Lite feature, which uses a linear inter...
2011-11-12 David WellsAdded 'reloadGridforceGrid' Tcl command.
2011-03-09 Jim PhillipsRemove "using namespace std" (or any other namespace...
2010-12-14 David WellsInitial check-in of multi-resolution gridforce.
2010-11-13 Chao MeiA completely fresh implementation of Parallel IO implem...
2010-06-29 Jim PhillipsMake langevin dynamics work with parallel I/O.
2010-06-09 David HardyAllow use of lone pairs outside of Drude model.
2010-04-26 Jim Phillipsfix extra bonds
2010-04-23 Osman SaroodParallelIO Checkin
2010-04-06 Jim PhillipsChange Index and related typedefs from short to int...
2010-03-04 Jim PhillipsDon't strip exclusions internal to hydrogen groups...
2010-02-05 Jim PhillipsFix compressed psf for migration groups. Only binary...
2010-02-04 Jim PhillipsUse migration groups based on lone pair hosts rather...
2010-02-03 Jim PhillipsEliminate global sorting with waters last and rename...
2010-01-24 David Hardyfor Drude model, don't count bonds to LPs as rigid...
2010-01-22 David HardyCan now set quartic restraints on Drude bonds to keep...
2010-01-19 David HardyFinished infrastructure for calculating anisotropic...
2010-01-17 David HardyDrude model: calculate Thole correction to electrostati...
2010-01-12 David Hardydon't allocate lphostIndexes array unless we need it...
2010-01-12 David HardyAdded Thole data type, build lists to index Thole and...
2009-12-17 David Hardyso that Drude data does not conflict with mem-opt builds
2009-09-20 David HardyRemoved earlier incorrect code to extend parent 1-3...
2009-09-16 David HardyPSF reader for Drude model, fix 1-3 exclusions for...
2009-07-20 Robert BrunnerThis code distributes the GridForce grid data among...
2009-06-03 Chris HarrisonUpdated src/Molecule.C, src/Molecule.h and src/NamdStat...
2009-05-21 Chao MeiFixed the bug for memory optimized version when extraBo...
2009-05-19 Jim PhillipsImplement modified 1-4 exclusions for CUDA. Only works...
2009-02-24 Chao Mei1. rewrite the module for compressing the psf file...
2009-02-18 Peter FreddolinoAdd tail corrections for water (necessary to get good...
2009-02-11 Chao MeiInterface changes for send_SimParameters/Parameters...
2008-12-15 Chao MeiAdded support for initializing Molecule and PDB object...
2008-10-23 Robert BrunnerChecking in multiple grid force code. Old grid force...
2008-10-16 Chao Mei1. added checking the compressed psf file format versio...
2008-10-01 David HardyCalculate number of degrees of freedom and related...
2008-09-28 Peter FreddolinoAllow TIP4P water to get proper parameters when used...
2008-09-26 David HardyDrude water model support enabled
2008-02-25 Peter FreddolinoAdd initial implementation of TIP4P water.
2007-12-11 Chao MeiFixed errors that multiple memory deletion operations...
2007-10-30 David Wells* Drastic structural changes to Gridforce code. There...
2007-10-09 David WellsUpdated Gridforces:
2007-10-02 Chao Meifixed a bug in retrieving the type of an atom in memory...
2007-09-25 David WellsSignificant changes to Gridforces using a new, more...
2007-09-05 David WellsFixed the way Gridforce interpolates boundary grid...
2007-08-03 Chao Mei1. Separate the deleting of mass and charge space for...
2007-08-02 Chao MeiAdd codes to support reading extra bonds from a separat...
2007-06-04 Abhinav Bhateleadded a function
2007-05-31 Chao MeiFreed unnecessary memory usage on each processor:
2007-05-30 Chao MeiOptimized memory usage for recording cluster informatio...
2007-05-30 Chao MeiRemove cluster building from build_lists_by_atom since...
2007-04-05 Chao MeiFixed a subtle bug in the memory-reduced version.
2007-04-04 Chao Meireduce memory usage further by deleting other each...
2007-03-30 Jim PhillipsAdded extraBonds and extraBondsFile config options...
2007-03-21 Chao MeiAdd assign operator for ExclusionCheck structure to...
2007-03-21 David WellsModifications to Gridforce:
2007-03-16 Chao Mei1. New structures for atom signature and exclusion...
2006-12-18 David WellsModifications for new feature, a Grid-based SMD feature...
2006-08-15 Jim PhillipsAdded support for "CMAP" crossterms from CHARMM31 force...
2004-08-06 Jim PhillipsAdded lesReduceTemp and lesReduceMass options to alter...
2004-07-26 Jim PhillipsAdded updateCharges Tcl command.
2004-04-15 Jim PhillipsFixed excessive memory usage by exclusion flag arrays...
2003-04-09 Barry IsralewitzBarry's torque application method. "Stirring" atoms...
2002-08-01 Jim PhillipsNew cluster code to handle structures with waters betwe...
2002-07-30 Jim PhillipsRemove spurious exclusions generated due to FEP or...
2002-05-24 Ilya Balabinadded local torqueing for atoms -- Ilya
2002-05-14 Ilya BalabinChanged atom dragging protocol and interface -- Ilya
2002-04-30 Jim PhillipsIsolated triplicate pointer/counter initialization...
2002-03-27 Jim PhillipswrapAll -> wraps any contiguous bonded cluster
2002-03-22 Jim PhillipsMultiple changes, including ability to disable temperat...
2002-02-21 Jim PhillipsIlya Balabin's dragging method.
2002-02-12 Jim PhillipsFree energy perturbation from Chris Chipot and Surjit...
2001-10-10 Paul GraysonThis gives NAMD the ability to load GROMACS topology...
2001-07-04 Fangqiang ZhuFor the feature of applying constant forces to atoms.
2001-06-27 Justin GullingsrudAdded excludeFromPressure option.
2001-06-13 Fangqiang ZhuAMBER file compatibility.
2000-09-13 Jim PhillipsFinished int to int32 changes.
2000-09-13 Jim PhillipsChanged int to int32 to save memory on T3E.
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