TIES MD APIο
+TIES MD can be used on the command line but for greater automation we also provide an API that exposes some options that
+may be routinely changed during setup.
APIο
+Here we detail all the options in the API and what should be passed. The options that were previously on the command line +can be passed into the TIES class like so:
+from TIES_MD import TIES
+md = TIES(cwd='./', windows_mask=[0,1], rep_id=0, exp_name='sys_solv')
+Once the TIES class is constructed the options that were previously in TIES.cfg can now be set as attributes of the TIES +class like so:
+# openmm.unit is needed to set values with units
+from openmm import unit
+
+#string for the molecular dynamics engine (openmm/namd2.14/namd3)
+md.engine = 'openmm'
+
+#Target temperature for the thermostat
+md.temperature = 300.0*unit.kelvin
+
+#Target pressure for barostat
+md.pressure = 1.0*unit.atmosphere
+
+#How much production sampling to run per alchemical window (4ns recommended)
+md.sampling_per_window = 0.04*unit.nanosecond
+
+#How much equilibration to run per alchemical window (2ns recommended)
+md.equili_per_window = 0.002*unit.nanosecond
+
+#List for which estimators to use.
+md.methods = ['FEP', 'TI']
+
+#How many total replicas of each window are run (we recommend at least 5).
+md.total_reps = 3
+
+#Boolean for if we will split all replicas into separate runs. (True for maximum parallelism)
+md.split_run = False
+
+#List for where in lambda schedule (0->1) should the electrostatic potentials begin, stop appearing.
+md.elec_edges = [0.5, 1.0]
+
+#List for where in lambda schedule (0->1) should the Lennard_Jones potentials begin, stop appearing.
+md.ster_edges = [0.0, 0.5]
+
+#List for the value the global controlling parameter takes in each window.
+md.global_lambdas = [0.00, 0.05, 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 0.95, 1.00]
+
+#String for name of the pdb file with constraints in the build directory, i.e. 'cons.pdb'
+md.constraint_file = None
+
+#String for column in pdb are constraints provided valid options are 'occupancy'/'beta_factor'.
+md.constraint_column = None
+
+#String for what input type is provided, only AMBER supported.
+md.input_type = 'AMBER'
+
+#list of x, y, z floats for box vectors of this simulation, unit Angstrom.
+md.cell_basis_vec1 = [34.55, 0.0, 0.0]
+md.cell_basis_vec2 = [-11.516722937414105, 32.574214501232206, 0.0]
+md.cell_basis_vec3 = [-11.516722937414105, -16.287105279373797, 28.21009840448772]
+Finally there are three additional options that donβt appear in TIES.cfg which are:
+#A header to a the submission script that will be written for this job.
+md.sub_header = """#Example script for Summit OpenMM
+#BSUB -P CHM155_001
+#BSUB -W 120
+#BSUB -nnodes 13
+#BSUB -alloc_flags "gpudefault smt1"
+#BSUB -J LIGPAIR
+#BSUB -o oLIGPAIR.%J
+#BSUB -e eLIGPAIR.%J"""
+
+#The prefix for the run line of this job.
+md.pre_run_line = 'jsrun --smpiargs="off" -n 1 -a 1 -c 1 -g 1 -b packed:1 '
+
+#the ties_md run line of this job.
+md.run_line = 'ties_md --config_file=$ties_dir/TIES.cfg --windows_mask=$lambda,$(expr $lambda + 1) --node_id=$i'
+The use of these three setting will produce a submission script which looks like:
+#!/bin/bash
+#Example script for Summit OpenMM
+#BSUB -P CHM155_001
+#BSUB -W 120
+#BSUB -nnodes 13
+#BSUB -alloc_flags "gpudefault smt1"
+#BSUB -J LIGPAIR
+#BSUB -o oLIGPAIR.%J
+#BSUB -e eLIGPAIR.%J
+
+export ties_dir="ties/ties-ligandA-ligandB/lig"
+cd $ties_dir
+
+for lambda in 0 1 2 3 4 5 6 7 8 9 10 11 12; do
+ for i in {0..5}; do
+ jsrun --smpiargs="off" -n 1 -a 1 -c 1 -g 1 -b packed:1 ties_md --config_file=$ties_dir/TIES.cfg --windows_mask=$lambda,$(expr $lambda + 1) --node_id=$i&
+ done
+ done
+wait
+If sub_header, pre_run_line and run_line are not set TIES_MD will make a best guess for a submission script.
+Ideally only small modification should be need to run using the best guess scripts. Any tweaks that are applied to get the
+scripts working can then be passed into sub_header, pre_run_line and run_line for future system setups. For
+general idea on how to make submission scripts see HPC Submission scripts.
