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__init__(self,
jobname,
cd_params,
force_field='OPLS3',
ensemble='NPT',
sim_time='5000',
rand_seed='2014',
buffer_width=0.0,
atom_mapping='',
ats=False,
lambda_windows=None,
charged_lambda_windows=None,
fep_convergence=0.0,
membrane=False)
Valid FF : OPLS_2005 OPLS3 CHARMM AMBER |
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| generate_complex_msj(self,
net_charge,
modify_dihe=False,
h_mass=False,
solvate=False,
ch=False,
minimize_volume=False) |
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| write_complex_msj(self,
modify_dihe=False,
h_mass=False,
solvate=False,
minimize_volume=False) |
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| generate_solvent_msj(self,
net_charge,
modify_dihe=False,
h_mass=False,
ch=False,
minimize_volume=False) |
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| write_solvent_msj(self,
modify_dihe=False,
h_mass=False,
minimize_volume=False) |
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| generate_subjob_msj(self,
buffer_width,
complex=False,
net_charge=False,
modify_dihe=False,
h_mass=False,
solvate=False,
ch=False,
minimize_volume=False) |
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| set_subjob_msj(self,
subjobmsj_contents,
buffer_width,
net_charge,
complex=False,
modify_dihe=False,
h_mass=False,
solvate=False,
core_hopping=False,
minimize_volume=False) |
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| generate_master_msj(self) |
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| get_fep_analysis_stage_number(self,
msj_filename) |
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| modify_fep_launcher_stage(self,
raw) |
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| modify_graph_stage(self,
raw) |
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| set_box_buffer_width(self,
raw,
width) |
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set_lambda_windows(self,
raw,
num_windows,
schedule_type='default') |
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| set_coul_correction(self,
raw) |
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| set_lambda_hopping(self,
raw,
h_mass=False) |
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Inherited from object:
__delattr__,
__format__,
__getattribute__,
__hash__,
__new__,
__reduce__,
__reduce_ex__,
__repr__,
__setattr__,
__sizeof__,
__str__,
__subclasshook__
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