Class VacuumMsjGenerator

        object --+    
                 |    
MapperMsjGenerator --+
                     |
                    VacuumMsjGenerator

Instance Methods

[hide private]

__init__(self, jobname, cd_params, force_field='OPLS3', sim_time='5000', rand_seed='2014', buffer_width=0.0, lambda_windows=None, charged_lambda_windows=None, fep_convergence=0.0)
Valid FF : OPLS_2005 OPLS3 CHARMM AMBER

write_vacuum_msj(self)

generate_vacuum_msj(self, net_charge=False)

set_subjob_msj(self, subjobmsj_contents, net_charge)

modify_fep_launcher_stage(self, raw)

modify_graph_stage(self, raw)

Inherited from MapperMsjGenerator: generate_complex_msj, generate_master_msj, generate_solvent_msj, generate_subjob_msj, get_fep_analysis_stage_number, set_box_buffer_width, set_coul_correction, set_cubic_box, set_ff, set_lambda_hopping, set_lambda_windows, write_complex_msj, write_master_msj, write_solvent_msj

Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __sizeof__, __str__, __subclasshook__

Properties

[hide private]

Inherited from object: __class__

Method Details

[hide private]

init(self, jobname, cd_params, force_field=`'OPLS3'`, sim_time=`'5000'`, rand_seed=`'2014'`, buffer_width=0.0, lambda_windows=None, charged_lambda_windows=None, fep_convergence=0.0)
(Constructor)

Valid FF : OPLS_2005 OPLS3 CHARMM AMBER

Overrides: object.__init__

Class VacuumMsjGenerator

__init__(self, jobname, cd_params, force_field='OPLS3', sim_time='5000', rand_seed='2014', buffer_width=0.0, lambda_windows=None, charged_lambda_windows=None, fep_convergence=0.0) (Constructor)

set_subjob_msj(self, subjobmsj_contents, net_charge)

modify_fep_launcher_stage(self, raw)

modify_graph_stage(self, raw)

init(self, jobname, cd_params, force_field=`'OPLS3'`, sim_time=`'5000'`, rand_seed=`'2014'`, buffer_width=0.0, lambda_windows=None, charged_lambda_windows=None, fep_convergence=0.0)
(Constructor)