###adaptivemastermsm.system package ###================================

###Submodules ###———-

adaptivemastermsm.system.system module

This file is part of the AdaptiveMasterMSM package.

class adaptivemastermsm.system.system.System(pdb, forcefield=None, water=None, topology=None, constraints=None)[source]

Bases: object

Create files to be able to run GROMACS

build_box(out='conf_edit.gro', d=1.0)[source]

Generates the box for the system

Parameters:d (float) – Distance between solute and box sides
gen_top(gro='conf.gro', top='topol.top')[source]

Generates topology from structure file.

ionize(neutral=True, conc=None, inp='conf_solv.gro', out='conf_solv_ions.gro', top='topol.top', tpr='ions.tpr')[source]

Adds ions for electroneutrality and / or target concentration.

Parameters:
  • neutral (bool) – Whether we neutralize the simulation box.
  • conc (float) – The target salt concentration in M.
solvate(inp='conf_edit.gro', out='conf_solv.gro', top='topol.top')[source]

Solvates the system using gmx solvate

adaptivemastermsm.system.system.check_gmx()[source]

Checks the available Gromacs version.

adaptivemastermsm.system.system_lib module

This file is part of the AdaptiveMasterMSM package.

adaptivemastermsm.system.system_lib.write_minimization_mdp(constraints='None')[source]

Module contents