| Adding code to deal with MPI_Send/Recv with data larger than the buffer. |
kd0kfo
as David Coss (portal2)
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about 14 years ago
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| Write a more streamlined sort algorithm for the XML node when MPI combines mmpbsa results. Hopefully, this will be much faster. |
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about 14 years ago
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| Updated mmpbsa_io::eof for changes to file reading. |
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about 14 years ago
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| Redesigned mmpbsa_io::seek so that it jumps through the trajectory file rather than reading data. This is much faster, although data begin skipped is no longer checked for validity. |
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about 14 years ago
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| n libmmpbsa: changed snapshot loading with sander files to give the option of either loading the whole file into memory OR leaving it on disk and loading snapshots when needed. If the sander_crd_stream pointer in the trajectory_t structure is null, then the disk is used. Otherwise, the stream (whether it is in memory or disk is irrelevant) will be used. Whether this should happen can be indicated with the "traj_in_memory" parameter. |
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about 14 years ago
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| Fixed typo in configure.ac |
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about 14 years ago
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| Increment version number for use of MPI |
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about 14 years ago
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| Fixed problem when there are more MPI nodes than snapshots. |
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about 14 years ago
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| Switched to storing data in XMLNode on master MPI node. |
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about 14 years ago
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| Successfully ran mmpbsa on 2 nodes with 2 snapshots. |
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about 14 years ago
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| Fixed frame number disagreement between mmpbsa.cpp and load_gmx_trr |
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about 14 years ago
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| Moved PDB code to mmpbsa_io and changed to atom_t & forcefield_t structure usage. |
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about 14 years ago
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| Checked each term in energy calculations for consistancy with tpr topology file. Seems consistant. |
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about 14 years ago
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| Increment Version number for the use of Multithreading and Amber & Gromacs file format reading. |
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about 14 years ago
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| Merged together multithreading and structure maded force fields, which allow for input formats other than sander. |
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about 14 years ago
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| Gromacs input seems to work, as well as previous sander input. |
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about 14 years ago
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| Have mmpbsa fully using structures. Not to integrate gromacs. |
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about 14 years ago
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| Added use of force field structures to MeadInterface |
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about 14 years ago
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| Added structure based energy calculations to EMap. |
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about 14 years ago
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| All of EmpEnerFun's energy calculations are performed in Energy.cpp. |
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about 14 years ago
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| Added atom information extraction for structures from EmpEnerFun. |
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about 14 years ago
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| Restructure Energy calculations and moved Internal energy routines to Energy.cpp. |
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about 14 years ago
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| MMPBSA can now read gromacs tpr and trr files and calculate energy. Units need to be adjusted since gromacs uses different units from amber. |
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about 14 years ago
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| Finished first implementation of gromax2prmtop. Testing needs to be done to 1.) see if it works and 2.) check for missing energy terms. |
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about 14 years ago
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| Added file with functions to import and convert various file formats. (work in progres) |
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about 14 years ago
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| Need to add gromacs .top file reader. Then put that data into SanderParm. |
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about 14 years ago
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| Commit work before moving to another computer. |
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about 14 years ago
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| mmpbsa_io now contains a function ( load_gmx_trr ) which will read a gromacs .trr file and store the coordinates of the specified frame (snap shot) in a valarray. |
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about 14 years ago
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| Merge branch 'master' into multi-thread |
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about 14 years ago
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| Removed molsurf from doxygen |
kd0kfo
as David Coss (stjudeathome2)
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about 14 years ago
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