TEMPLATE_SYSTEM_NAME

Requirements

• TEMPLATE_PROJECT_PREFIX
• conda environment

Environment variable to detect project directory path

TEMPLATE_PROJECT_PREFIX to detect project directory.

If this repository located in /home/flat35hd99/ytva/ and the directory name is dark (See below tree), TEMPLATE_PROJECT_PREFIX=/home/flat35hd99/ytva/dark. Don't add slash ("/") in the last of the variable.

I recommend you to add export TEMPLATE_PROJECT_PREFIX=/path/to/directory into .bashrc or other script that is loaded in initialization of CLI.

ytva/
├── dark <- This repository
│   ├── 0structure
│   ├── 1minimization
│   ├── 2equilibrium
│   ├── 3sampling
│   ├── 4nve
│   ├── 5heat_flux
│   ├── 6heat_conductivity
│   ├── FMN
│   └── README.md
└── light

conda environment

# Install miniconda in $HOME/miniconda3_x86_64

# If you want to install other place,
# please change util/load_curp

# conda environment name to intall curp
env_name=py2curp

# If possible, please use newer versions without python
conda create -n $env_name python=2.7 netcdf4=1.4.2 pygraphviz=1.3
conda activate $env_name
pip install curp==1.3.1

Process

1. 0structure
   1. create_amber_input.sh
   2. create_atomgroup_sidechain.sh
2. 1minimization
   1. pjsub job.sh
3. 2equilibrium
   1. submit.sh 0 4
4. 3sampling
   1. submit.sh 0 4
5. 4nve
   1. submit.sh 0 49
   2. submit_utility.sh 0 49 on IMS
6. 5curp
   1. ./generate_representation_of_grouppair.sh on IMS.
   2. submit.sh 0 49 residue and submit.sh 0 49 side on IMS