| Added files needed by make that were left out of the previous commit. |
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over 14 years ago
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| Added BOINC tags to configure.ac and Makefile.am |
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over 14 years ago
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| Restructored the library, placing everything not centered around the main() function in mmpbsa.cpp, in the "mmpbsa" namespace. Also SanderParm was placed in its own c++ file. Both of these choices are based on using mmpbsa as a library with other programs which will be developed later. |
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over 14 years ago
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| Renamed Energy.* to EmpEnerFun.* There may be more pure energy classes later with MD calculations. Therefore, I may not want to call this Energy. |
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over 14 years ago
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| Information file updates. Nothing major. |
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over 14 years ago
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| Included setup and updated INSTALL accordingly |
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over 14 years ago
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| Revert "Added install-sh" |
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over 14 years ago
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| Revert "Added configure and setup. setup can be used to reproduce configure using configure.ac and autotools" |
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over 14 years ago
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| Added install-sh |
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over 14 years ago
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| Added configure and setup. setup can be used to reproduce configure using configure.ac and autotools |
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over 14 years ago
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| Setup MMPBSA to use autotools. As the project has grown, making a Makefile has likewise become complex. Therefore using autotools is a natural choice. As a result, the directory try has been restructured as well. |
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over 14 years ago
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| Updated Makefile for XMLParser |
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over 14 years ago
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| Added checkpointing, saving the state in an XML file. BOINC checkpointing functions are included, but are only used if the "__USE_BOINC__" preprocessor flag is set at compile time. |
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over 14 years ago
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| Did some serious documenting. |
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over 14 years ago
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| Separated Complex, Receptor and Ligand outputting. Doing so may help monitor and pause the application better (thinking ahead to the grid). |
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over 14 years ago
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| Fixed typo. |
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over 14 years ago
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| Added command line parameter "snap_list" that will allow the use to calculate specific snapshot energies. This is a good idea for parallel computing, since it will allow one to calculate different snapshots on different nodes. |
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over 14 years ago
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| Restructured EmpEnerFun. |
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over 14 years ago
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| Moved main.cpp to mmpbsa.cpp. Might make other "main" classes. In which case, main.cpp will no longer make sense. |
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over 14 years ago
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| Made command line use more natural. All that is left in that respect is creating a list of which molecules belong to the receptor and which belong to the ligand. The implementation of this will depend in part on how it will be used later, .e. should it be a csv list. |
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over 14 years ago
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| Updated gnu make file. Added a better handler for EOF of trajectory file in main.cpp, adding an UNEXPECTED_EOF error type. |
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over 14 years ago
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| Finished mmpbsa. Tested the program and the results match those of the python version of mmpbsa. |
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over 14 years ago
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| Updated Makefile.mmpbsa for the new template instantation class. |
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over 14 years ago
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| Successfully added (and tested) adding MEAD's PB solver. All that remains for mmpbsa calculations is SA calculation. |
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over 14 years ago
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| Added MeadInterface class. Added PB functionality to the project. Test + SA-functionality remain. |
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over 14 years ago
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| Complete testing of Energy data reading, stripping and reporting. Results match previous outputs from python code. |
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over 14 years ago
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| Added stripEnerFun. Debugging should follow. |
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over 14 years ago
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| Finished the EmpEnerFun Loading process. Test loaded an energy function with a solvent. Still need to test without a solvent to see if BondWalker works correctly. |
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over 14 years ago
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| Energy.cpp compiles. Whole set builds. Needs testing. |
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over 14 years ago
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| Added mmpbsa_utils, which is a namespace that holds various utility functions that are needed in the other classes. Created an mmpbsa_t type using typedef. This was done so that precision, i.e. float versus double, may be adjusted. |
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over 14 years ago
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