schrodinger.application.desmond.fep_scholar_msj_generator module¶
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class
schrodinger.application.desmond.fep_scholar_msj_generator.
FEPScholarMsjGenerator
(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)¶ Bases:
object
This class generates master msj file that manages both solvent and complex legs of the FEP simulation.
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__init__
(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
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write_complex_msj
()¶
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write_solvent_msj
()¶
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write_master_msj
()¶
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generate_subjob_msj
(fname, buffer_width, MSJ_TEMPLATE=None)¶
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generate_master_msj
()¶
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modify_multisim_stage
(raw)¶ Method modifies ‘multisim’ stage in the master msj file
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get_total_proc
()¶
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static
set_box_buffer_width
(raw, width)¶
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set_ff
(raw)¶
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set_lambda_hopping
(raw)¶
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