Class FEPScholarMsjGenerator

object --+
         |
        FEPScholarMsjGenerator

This class generates master msj file that manages both solvent and complex legs of the FEP simulation.

Instance Methods

[hide private]

__init__(self, jobname, cd_params, structure_fname, force_field='OPLS_2005', ensemble='NPT', sim_time='5000', rand_seed='2015', complex_box_buffer_width=5.0, trj_interval=24.0)
Valid FF : OPLS_2005 CHARMM AMBER

write_complex_msj(self)

write_solvent_msj(self)

write_master_msj(self)

generate_subjob_msj(self, fname, buffer_width, MSJ_TEMPLATE=None)

generate_master_msj(self)

modify_multisim_stage(self, raw)
Method modifies 'multisim' stage in the master msj file

get_total_proc(self)

set_ff(self, raw)

set_lambda_hopping(self, raw)

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

Static Methods

[hide private]

set_box_buffer_width(raw, width)

Properties

[hide private]

Inherited from object: __class__

Method Details

[hide private]

init(self, jobname, cd_params, structure_fname, force_field=`'OPLS_2005'`, ensemble=`'NPT'`, sim_time=`'5000'`, rand_seed=`'2015'`, complex_box_buffer_width=5.0, trj_interval=24.0)
(Constructor)

Valid FF : OPLS_2005 CHARMM AMBER

Overrides: object.__init__

Class FEPScholarMsjGenerator

__init__(self, jobname, cd_params, structure_fname, force_field='OPLS_2005', ensemble='NPT', sim_time='5000', rand_seed='2015', complex_box_buffer_width=5.0, trj_interval=24.0) (Constructor)

init(self, jobname, cd_params, structure_fname, force_field=`'OPLS_2005'`, ensemble=`'NPT'`, sim_time=`'5000'`, rand_seed=`'2015'`, complex_box_buffer_width=5.0, trj_interval=24.0)
(Constructor)