###adaptivemastermsm.system package ###================================
###Submodules ###———-
adaptivemastermsm.system.system module¶
This file is part of the AdaptiveMasterMSM package.
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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
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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
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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.
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adaptivemastermsm.system.system_lib module¶
This file is part of the AdaptiveMasterMSM package.