schrodinger.application.matsci.equilibrium_md module

Equilibrium molecular dynamics classes/function shared by transport property calculations using Einstein and Green-Kubo methods.

Copyright Schrodinger, LLC. All rights reserved.

schrodinger.application.matsci.equilibrium_md.check_file_exist(path_file)

Check and find the path/file on the host

Parameters:path_file (filename with path) – string
Return type:None or str
Returns:None if the file cannot be located
schrodinger.application.matsci.equilibrium_md.get_md_results(basename, log, log_error, opts, **kwargs)

From parsed options, setup and run md simulation.

Parameters:
  • basename (str) – basename for md simulation job
  • log (function) – log information
  • log_error (function) – log error information and exit
  • opts (Named tuple) – The parsed command line option
  • kwargs (dict) – extra options to control md simulation
Return type:

str, str, str or None
Returns:

output cms, trj folder, and enegrp_file
schrodinger.application.matsci.equilibrium_md.find_head_tail(struct, atom_ids=None)

Find the head and tail atoms of the longest path. If multiple longest paths are found, rank those longest paths by the head atom ids and then tail atom ids. Choose the longest path with the smallest head/tail atom ids.

Parameters:
  • struct (the structure containing the target molecule.) – structure.Structure
  • atom_ids (atom ids of the target molecule. If None, all the atoms in the struct are used.) – list of int or None
Return type:

int, int
Returns:

atom ids for head and tail atoms
schrodinger.application.matsci.equilibrium_md.setup_md_job(name_base, icms, md_time, md_timestep, md_emsemble, md_temperature, md_pressure, trj_interval, md_save_trj, random_seed, gpu, procs, write_vel=False, md_enegry_interval=None, md_save_enegrp=False, energy_groups=[])

Write the .msj file and form the command for running the molecular dynamics simulation at a specific temperature.

Parameters:
  • name_base (base name for the md job) – str
  • icms (input cms filename) – str
  • md_time (md simulation time in ps) – float
  • md_timestep (md timestep in ps) – float
  • md_emsemble (md ensemble) – str
  • md_temperature (md temperature in K) – float
  • md_pressure (md pressure in bar) – float
  • trj_interval (time interval for trj output in ps) – float
  • md_save_trj (save trj folder, if True) – bool
  • random_seed (int) – Seed for random number generator used in simulation
  • gpu (request gpu, if True) – bool
  • procs (number of processors) – int
  • write_vel (record velocity in trj frame, if True) – bool
  • md_enegry_interval (time interval for energy group output) – float or None
  • md_save_enegrp (save the enegry_file, if True) – bool
  • energy_groups (list of keywords for desmond energy_groups) – list of str
Return type:

str, str, str, str
Returns:

cmd command to submit md, output cms, trj folder, enegrp file
schrodinger.application.matsci.equilibrium_md.trim_parser_skip_md(options, extra=[])

If md is skipped, delete any options for setting up molecular dynamics simulation.

Parameters:
  • options (Parsed command options) – Named tuple
  • extra (extra flags to be deleted) – list of str
Return type:

options: Named tuple
Returns:

Parsed command options with no md flags
schrodinger.application.matsci.equilibrium_md.add_parser_opts(parser, final_prop, mid_prop, use_tau=True, extra_options=None)

Add all necessary parser arguments for setting up a MD simulation and optional arguments for certain green-kubo property calculation.

Parameters:
  • parser (argparse.ArgumentParser) – The parser for error information
  • final_prop (the final property needs to be calculated) – str
  • mid_prop (the property needs to be calculated before the final prop) – str
  • use_tau (Tau limits are added, if True) – bool
  • extra_options (extra options can be added according to these keywords) – None or list of str
schrodinger.application.matsci.equilibrium_md.check_options(opts, parser, option_flag, min_data_point, check_tau=True)

Validate the options.

Parameters:
  • opts (Named tuple) – The parsed command line options
  • parser (argparser.ArgumentParser) – parser to log error information
  • option_flag (str) – time interval is defined by this flag
  • check_tau (bool) – validate tau range against available time range
  • min_data_point (int) – minimum required data point
class schrodinger.application.matsci.equilibrium_md.EquilibriumMdBase(icms_name)

Bases: object

This is a base class for equilibrium MD subclass, and should be not be instantiated directly.

checkSetTimeInterval(time_intervals=None)

Time interval must be the same for all trajectery.

Parameters:time_intervals (list or None) – time intervals between every two frames.
checkConstantVol(allow_npt=True)

Calculate volume and check whether it changes.

Parameters:allow_npt (bool) – allow volume to change, if True
calDensity()

Caluate the average system density.

savePropAndCms()

Save properties to cms model, delete trj information if needed, and write out cms file.

class schrodinger.application.matsci.equilibrium_md.TrjBase(icms_name)

Bases: schrodinger.application.matsci.equilibrium_md.EquilibriumMdBase

This is a base class for equilibrium MD subclass that uses trajectory, and should be not be instantiated directly.

readTrj(make_whole=False)

Read trj frames from trj folder.

Parameters:make_whole (bool) – if True, bond across PBCs are fixed so that two bonded particles won’t be on opposite sides of the system
trajFrames(make_whole=False)

Fix pbc bonds (if needed), yield the trajectory frame, and garbage-collect to release the occupied memory.

Parameters:make_whole (bool) – if True, bond across PBCs are fixed so that two bonded particles won’t be on opposite sides of the system
Return type:schrodinger.application.desmond.packages.traj.frame
Returns:a trajectory frame
checkTau(total_trj_frame_num, min_tau_data_point)

Check whether trj frame number is large enough.

Parameters:
  • total_trj_frame_num (number of total data point) – int
  • min_tau_data_point (minimum requested data) – int
checkVel()

Check whether each frame contains velocity information.

class schrodinger.application.matsci.equilibrium_md.MixInBlockStd

Bases: object

This is a base class for dividing long simulation into blocks to get standard deviation, and should be not be instantiated directly.

checkBlockTau(total_step_num, min_tau_data_point)

Chech whether there are minimum data points between Tau start and end.

Parameters:
  • total_step_num (number of total data point) – int
  • min_tau_data_point (minimum requested data) – int