ptc-cmc / terminal_groups_mixed

Screening monolayer terminal groups for influences on lubrication

This repository is set-up nearly identical to that used for screening of chemically-identical monolayer systems (summeraz/terminal_group_screening); however, here systems feature two contacting monolayers with different chemistries.

Installation/Set-up

Download and install anaconda

Note: I did this and in the /ccs/proj/ directory on Titan

Create a new environment (3.5 is preferred)

>> conda create --name myconda python=3.5

Activate the environment

>> conda activate myconda

Note: You may have to first append to your path the directory where anaconda is located, e.g.

>> export PATH=/ccs/proj/xxx000/anaconda/titan/bin:$PATH

Clone and install atools

commit 320523d91535e497b5dbc2b6a821cc0453985055

>> git clone https://github.com/PTC-CMC/atools.git

>> pip install .

Clone and install mbuild

commit fa2bc651823d8c0a93cac8721e0abf10a7b5e168

>> git clone https://github.com/mosdef-hub/mbuild.git

>> pip install .

Clone and install foyer

commit 1aa97bbebed22c94ad8d9d68486fbdbe7a3bd6d7

>> git clone https://github.com/mosdef-hub/foyer.git

>> pip install .

Install signac-flow

>> conda install signac-flow=0.5.4 -c glotzer

Install dependencies

Note: If mBuild and Foyer are installed via conda or pip, these dependencies should be installed automatically.

>> conda config --add channels omnia mosdef
>> conda install lxml requests networkx mdtraj oset parmed openmm plyplus
>> pip install mdanalysis

Clone the terminal_groups_mixed repository

>> git clone https://github.com/PTC-CMC/terminal_groups_mixed.git

Initialize the project

Note: All flow commands must be performed from the project root directory.

Note: The -n 5 1 signifies that five statepoints will be created for each parameter state, each with a different random seed (incrementing from 1)

>> python src/init.py -n 5 1

---

Signac workflow

Initialize/construct systems

This will submit jobs in bundles of 6 statepoints to be executed on a single node. Although each node contains 16 processors, memory issues limit the number of simultaneous systems that can be initialized.

>> python src/project.py submit -o initialize --bundle 6 --nn 1 -w 0.5

Run minimization in LAMMPS to fix overlaps

>> python src/project.py submit -o fix_overlaps --bundle 400 --nn 400 -w 1

Convert last frame of LAMMPS trajectory to a GROMACS structure file

>> python src/project.py submit -o lammps_to_gmx --bundle 48 --nn 3 -w 0.5

Create TPR file for GROMACS energy minimization

>> python src/project.py submit -o minimize_grompp --bundle 400 --nn 400 -w 0.5

Run GROMACS energy minimization

>> python src/project.py submit -o minimize --bundle 400 --nn 400 -w 0.5

Create TPR file for GROMACS NVT equilibration

>> python src/project.py submit -o equilibrate_grompp --bundle 400 --nn 400 -w 0.5

Run GROMACS NVT equilibration

>> python src/project.py submit -o equilibrate --bundle 400 --nn 400 -w 2

Create TPR file for GROMACS compression

>> python src/project.py submit -o compress_grompp --bundle 400 --nn 400 -w 0.5

Run GROMACS compression

>> python src/project.py submit -o compress --bundle 400 --nn 400 -w 1

Create TPR file for GROMACS shear at a normal load of 5nN

>> python src/project.py submit -o shear_5nN_grompp --bundle 400 --nn 400 -w 0.5

Run GROMACS shear at a normal load of 5nN

>> python src/project.py submit -o shear_5nN --bundle 400 --nn 400 -w 4

Create TPR file for GROMACS shear at a normal load of 15nN

>> python src/project.py submit -o shear_15nN_grompp --bundle 400 --nn 400 -w 0.5

Run GROMACS shear at a normal load of 15nN

>> python src/project.py submit -o shear_15nN --bundle 400 --nn 400 -w 4

Create TPR file for GROMACS shear at a normal load of 25nN

>> python src/project.py submit -o shear_25nN_grompp --bundle 400 --nn 400 -w 0.5

Run GROMACS shear at a normal load of 25nN

>> python src/project.py submit -o shear_25nN --bundle 400 --nn 400 -w 4

---

Post-processing/Analysis

Unwrap trajectories

>> python src/analysis.py submit -o unwrap_shear_5nN --bundle 48 --nn 3 -w 1
>> python src/analysis.py submit -o unwrap_shear_15nN --bundle 48 --nn 3 -w 1
>> python src/analysis.py submit -o unwrap_shear_25nN --bundle 48 --nn 3 -w 1

Calculate friction forces for each shear trajectory

>> python src/analysis.py submit -o calc_friction --bundle 48 --nn 3 -w 1

Calculate monolayer nematic order for each shear trajectory

>> python src/analysis.py submit -o calc_S2_shear --bundle 18 --nn 3 -w 1

Log COF

>> python src/analysis.py submit -o log_cof --bundle 48 --nn 3 -w 1