PoreSim

Simulation with molecules only in the pore

import poresim as ps

Set job inputs for your working station

Example Bash file for Horeka:

#!/bin/bash 
#SBATCH --nodes=SIMULATIONNODES 
#SBATCH --ntasks-per-node=SIMULATIONPROCS 
#SBATCH --time=SIMULATIONTIME 
#SBATCH --job-name=SIMULATIONLABEL 
#SBATCH --error=SIMULATIONLABEL.e.%J 
#SBATCH --output=SIMULATIONLABEL.o.%J 

module load chem/gromacs/2019.6_cpu 

COMMANDCHANGEDIR

COMMANDGROMACS

Simulation inputs

cpu = 75
job = {"min": {"file": "data/bash.sh", "nodes": 1, "np": cpu, "wall": "24:00:00"},
       "nvt": {"file": "data/bash.sh", "nodes": 5, "np": cpu, "wall": "24:00:00"},
       "run": {"file": "data/bash.sh", "maxh": 24, "nodes": 5, "np": cpu, "runs": 15, "wall": "24:00:00"}}

param = {"min": {"file": "../Simulation_Inputs/Pore/pore_eq_min.mdp"},
         "nvt": {"file": "../Simulation_Inputs/Pore/pore_eq_nvt.mdp", "param": {"NUMBEROFSTEPS": 500000, "TEMPERATURE_VAL": 353.15}},
         "run": {"file": "../Simulation_Inputs/Pore/pore_prod_run.mdp", "param": {"NUMBEROFSTEPS": 200000000, "TEMPERATURE_VAL": 353.15}}}

cluster_horeka = {"address": "",                    
                  "directory": "xxx",        
                  "queuing": {"add_np": False, "mpi": "$DO_PARALLEL", "shell": "horeka.sh", "submit": "sbatch -p cpuonly "}}

Create a box object with the molecules contained in your system

pores = ps.Box("conf4")
pores.set_label("conf4")
pores.add_box("../PoreMS/pore.gro")
pores.add_pore("../PoreMS/pore.yml")
pores.add_struct("mol_list", "../PoreMS/pore.obj")

# Add gro files 
pores.add_mol("CAT", "../Molecules/cat.gro", inp=4, section="pore",  kwargs_gmx={"-try": 1000})
pores.add_mol("EDC", "../Molecules/edc.gro", inp=18, section="res",  kwargs_gmx={"-try": 1000})
pores.add_mol("IM", "../Molecules/im.gro", inp=311, section="pore", kwargs_gmx={"-try": 50000} )
pores.add_mol("BF4", "../Molecules/bf4.gro", inp=600, section="pore",  kwargs_gmx={"-try": 50000})
pores.add_mol("HEP", "../Molecules/1-heptane.gro", inp="fill", mass = 100.21, auto_dens=629.595, section = "res", kwargs_gmx={"-try":1000} )


# Add top files 
pores.add_topol("../PoreMS/master_topol_pore.top", "master")
pores.add_topol("../Topologies/forcefield_new_red.itp","top")
pores.add_topol("../Topologies/ffnonbonded_new_red.itp","top")
pores.add_topol("../Topologies/ffbonded_new.itp","top")
pores.add_topol("../Surfaces_Molecules/tms.itp","top")
pores.add_topol("../Surfaces_Molecules/tmsg.itp", "top")
pores.add_topol("../PoreMS/grid.itp", "top")
pores.add_topol("../Topologies/cat.itp", "top")
pores.add_topol("../Topologies/bf4.itp", "top")
pores.add_topol("../Topologies/im.itp", "top")
pores.add_topol("../Surfaces_Molecules/im_img_surface.itp", "top")
pores.add_topol("../Topologies/1-heptane.itp", "top")
pores.add_topol("../Topologies/educt_oplsaa.itp", "top")

pores.set_job(job)
pores.set_param(param)

:::{note} If you only want to put molecules into the pore, it is better to add the larger molecules first to make sure that Gromacs can get them into the pore. :::

Create simulation objects and generate folder structure

sim = ps.Simulate("Simulation/pore/conf4-r", pores)  # Single
sim.set_cluster(cluster_horeka)
sim.generate()

Finished simulation folder - conf4-r ...

Image of the system after filling the box

Inside view of the pore after running construct.sh. Colour code: catalyst, red; ionic anion, orange; ionic kation (on pore surface), green; ionic kation, blue; rectant, grey; heptane not shown.

:::{figure} /pics/pore_il.svg :align: center :width: 70% :::

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