Calculation of free energy of evaporization¶

[1]:

import os
from pygromos.files.forcefield.gromos.gromosff import GromosFF
from pygromos.files.gromos_system.gromos_system import Gromos_System
from pygromos.simulations.approaches.hvap_calculation.hvap_calculation import Hvap_calculation
from pygromos.data.simulation_parameters_templates import template_sd

[2]:

work_dir=os.getcwd()+"/example_files/Hvap_files/"

[3]:

ff = GromosFF(name="54A7")

[4]:

groSys = Gromos_System(work_folder=work_dir+"init/", system_name="Hvap_test", in_smiles="O", in_residue_list=["H2O"],
                       auto_convert=True, forcefield=ff, in_imd_path=template_sd)

[5]:

hvap_sys=Hvap_calculation(input_system=groSys, work_folder=work_dir+"hvap", forcefield=ff, system_name="test", useGromosPlsPls=True)

/home/mlehner/PyGromosTools/pygromos/simulations/approaches/hvap_calculation/hvap_calculation.py:99: UserWarning: Folder does already exist
  warnings.warn("Folder does already exist")

[6]:

hvap_sys.create_liq()

ran_box @topo /home/mlehner/PyGromosTools/docs/sphinx_project/Examples/example_files/Hvap_files/hvap/test_gas/Hvap_test.top @pbc r @pos /home/mlehner/PyGromosTools/docs/sphinx_project/Examples/example_files/Hvap_files/hvap/test_gas/Hvap_test.cnf @nsm 512 @dens 489.99999999999994  @thresh 0.12 @layer  > /home/mlehner/PyGromosTools/docs/sphinx_project/Examples/example_files/Hvap_files/hvap/temp.cnf

[7]:

# reduce number of steps for demonstration purposes
hvap_sys.imd_gas_eq.STEP.NSTLIM = 10
hvap_sys.imd_gas_sd.STEP.NSTLIM = 100

[8]:

hvap_sys.run_gas()

################################################################################

1_emin
################################################################################

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FOUND RESULT: /home/mlehner/PyGromosTools/docs/sphinx_project/Examples/example_files/Hvap_files/hvap/test_gas/1_emin/analysis/data/1_emin.cnf
 GOING TO SKIPT THIS SUBMISSION!
################################################################################

2_eq
################################################################################

============================================================
FOUND RESULT: /home/mlehner/PyGromosTools/docs/sphinx_project/Examples/example_files/Hvap_files/hvap/test_gas/2_eq/analysis/data/2_eq.cnf
 GOING TO SKIPT THIS SUBMISSION!
################################################################################

3_sd
################################################################################

============================================================
FOUND RESULT: /home/mlehner/PyGromosTools/docs/sphinx_project/Examples/example_files/Hvap_files/hvap/test_gas/3_sd/analysis/data/3_sd.cnf
 GOING TO SKIPT THIS SUBMISSION!

[9]:

# reduce number of steps for demonstration purposes
hvap_sys.imd_liq_eq.STEP.NSTLIM = 10
hvap_sys.imd_liq_md.STEP.NSTLIM = 100
hvap_sys.imd_liq_md.WRITETRAJ.NTWE = 40

[10]:

hvap_sys.run_liq()

################################################################################

1_emin
################################################################################

============================================================
FOUND RESULT: /home/mlehner/PyGromosTools/docs/sphinx_project/Examples/example_files/Hvap_files/hvap/test_liq/1_emin/analysis/data/1_emin.cnf
 GOING TO SKIPT THIS SUBMISSION!
################################################################################

2_eq
################################################################################

============================================================
FOUND RESULT: /home/mlehner/PyGromosTools/docs/sphinx_project/Examples/example_files/Hvap_files/hvap/test_liq/2_eq/analysis/data/2_eq.cnf
 GOING TO SKIPT THIS SUBMISSION!
################################################################################

3_sd
################################################################################

============================================================
FOUND RESULT: /home/mlehner/PyGromosTools/docs/sphinx_project/Examples/example_files/Hvap_files/hvap/test_liq/3_sd/analysis/data/3_sd.cnf
 GOING TO SKIPT THIS SUBMISSION!

[11]:

hvap_sys.calc_hvap()

[11]:

27.752725812108782

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