reanalyze_fep.py Command Help

Command: $SCHRODINGER/run reanalyze_fep.py

usage: reanalyze_fep.py [-h] [-b BEGIN_TIME] [-e END_TIME] [-o OUT_FMP]
                        [-i IN_FMP] [-num-procs NUM_PROCS] [-update-sid]
                        [-fast] [-debug]
                        [checkpoint ...]

Reanalyze fep simulations with given begin-time and end-time (ps).
You have to be in the root folder of output folder. This script assumes
that user's original fmp output is <jobname>_out.fmp

Example:

    $SCHRODINGER/run reanalyze_fep.py job-multisim_checkpoint -o new.fmp -b 2000 -e 4000

Running the script in fast mode (`-fast`) only requires the input FMP file and
desired end time.  It uses existing precalculated forward dG values from the
SID report, therefore cannot be combined with `-begin-time`.  The dG values for
complex and solvent legs (solvent and fragment legs for `prm_thermostability`
FEP type) are estimated from the relatively coarsely sampled timeseries data in
the SID report by linear interpolation.

Example:

    $SCHRODINGER/run reanalyze_fep.py -fast -i original_out.fmp -o new.fmp -e 4000

This script can also work with extended simulation by providing more checkpoint files

Example:

    $SCHRODINGER/run reanalyze_fep.py job-0-multisim_checkpoint job-1-multisim_checkpoint -o new.fmp -b 2000 -e 4000

    In this case, begin-time and end-time will reflect the accumulated data from different
    runs. The order of checkpoint files does matter.

positional arguments:
  checkpoint            Any number of `fep_plus`-output checkpoint files.  Required except in `-fast` mode with `-i IN_FMP`

options:
  -h, --help            show this help message and exit
  -b BEGIN_TIME, -begin-time BEGIN_TIME
                        Begin time (ps). Default is 100.0
  -e END_TIME, -end-time END_TIME
                        End time (ps). Default is the end of simulation
  -o OUT_FMP            Output fmp file. Default is <jobname>_new_out.fmp
  -i IN_FMP             Input fmp file. Default is <jobname>_out.fmp
  -num-procs NUM_PROCS  Number of processors to be used. A negative value will trigger using all available cores
  -update-sid
  -fast                 Interpolate dG and dG error values from timeseries data from existing SID report data stored in the input FMP file.  Cannot be used with `-b[egin-time]` or `-update-sid`; `-num-procs` will be ignored if given
  -debug