Screening monolayer terminal groups with three new chemistries

These simulations are with chemically identical films.

Installation/Set-up

Download and install anaconda

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

Note: Titan has been decomissioned as of August 01, 2019; some of these commands might not work on other systems without editing.

Create a new environment (3.5 is preferred)

>> conda create --name myconda python=3.5

Activate the environment

>> source 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 caa89f99a07c84be4c457378138105100eaa9dfb

>> 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_group_mixed_original_16_new_3 repository

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

Initialize the project

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

Note: The -n 3 -c 17 1 signifies that three statepoints will be created for each parameter state, with an alkane backbone of 17 carbons, each with a different random seed (incrementing from 1)

>> python src/init.py -n 3 -c 17 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_system --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 lmp_to_gmx --bundle 48 --nn 3 -w 0.5

Create TPR file for GROMACS energy minimization

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

Run GROMACS energy minimization

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

Create TPR file for GROMACS NVT equilibration

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

Run GROMACS NVT equilibration

>> python src/project.py submit -o nvt_mdrun --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 mdrun_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

Note: Shear was originally performed for 5ns and then extended another 5ns. The MDP files have been updated to include the full 10ns now.

>> python src/project.py submit -o mdrun_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 mdrun_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 mdrun_shear_25nN --bundle 400 --nn 400 -w 4

NOTE: If the simulations do not complete in the hours provided, concatenating the TRR files is necessary.

This is easier to do through the trjcat command from command line GROMACS.

gmx_mpi trjcat -f shear_5nN*.trr -o shear_5nN_combined.trr

gmx_mpi trjcat -f shear_15nN*.trr -o shear_15nN_combined.trr

gmx_mpi trjcat -f shear_25nN*.trr -o shear_25nN_combined.trr

---

Post-processing/Analysis

Calculate friction forces for each shear trajectory

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

Log COF

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