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UPDATES
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UPDATE HISTORY (ZIP)
--------------------
26/01/2015
- Fixed plotting to take selected steps (when simulation is not finished but we want to plot some data).
20/01/2015
- Fixed compatibility issues with python2.6
- Fixed compatibility issues with cpptraj
11/03/2015
- Added trim tool function
- Added replica creation from TOP+CRD
- Added --ref option to align command
- Added iwrap option to mdsettings. It will be now 0 by default (instead of 1) to avoid problems with check_com.sh file when using restraints.
- Fixed several bugs in replica volume calculation, pdb renumbering for large PDBs (>9999 residues), Density calculation on partial trajectories.
- Added Replica function to calculate last completed step in production
17/03/2015
- updated VERSION 0.1.6
- Added --ref option to density command to build density on subregion of space or to follow --ref option in alignment
- Added hotspots create_min action to use minimum search method instead of clustering one to locate hotspots
- Modified Projects.py to add iwrap attribute to replicas that don't have it (for back compatibility)
18/03/2015
- Improved solvent printing to add number of snapshots to obtain 1 expected count per probe.
- Added 'stepselection' to energy conversion to correctly calculated number of snapshots when a subset of the trajectory was used in density calculation.
23/03/2015
- Initial OpenMM support
07/04/2015
- Merged OpenMM support fork (Mark J. Williamson work) to master.
- Changed version to 0.2.0
09/04/2015
- Moved simulation volume functions from Energy.py to Checkers of each MD program.
- Fixed bug in replica number of snapshots calculation (failing when npt_prod_steps != 1 ns).
- Modified ratio-correction in Energy.py to allow pure solvent boxes (e.g. ETA 100%).
- Modified version numbering control
20/04/2015
- Added function to compute similarity to GridsManager (cleaner and better documented than that in GridData).
07/07/2015
- Fixed bug in PDB magicFit function causing maximum recursion error when too many water molecules are present. Added mask to the alignment.
- Fixed some bugs in grid comparison function.