Calculates the heat capacity as a function of temperature for a simulation of 8 proteins.
Files: analyzer.py Calculates heat capacity as a function of temperature from only a few states. in_mbar input files out_mbar output files
This data set originally caused a crash because the dynamic range of the free energies was too large when the weights were stored in non-logarithmic form.
Files to be analyzed using alchemical-gromacs.py
Call is
python alchemical-gromacs.py -d X -p dhdl -t 298
where X is the relevant directory.
Directory contains: 11states50ns/ dhdl..xvg out11states.txt 38states/ dhdl..xvg out38states.txt
From Cassiano Gomes-Aimoli and Ed Maginn.
Uses MBAR to interpolate the properties of TraPPE methane force field in two dimensions. See gas-properties README for more information. Two notes; requires a lot of memory (>6GB) so is a good stress test, and hopefully we can get the memory required down. Also, requires the installation of the included uncertainties package to run the analysis.
The driver scripts 8proteins/analyzer.py and gas-properties/run_mbar_all.py have an optional parameter DUMP_DATA_HDF at the top of each script. By setting this flag to True and running, you can save a machine-readable version of the dataset to be used for testing and benchmarking your pymbar installation.