siminp.yaml

# =============================================================================
# General specifications for simulation input generation
# =============================================================================

# =============================================================================
# Required Parameters
# =============================================================================

# Simulation run sequence:

# Available default run specifications:
# EM - energy minimisation
# EQ_NVT_F - equilibration in NVT ensemble and fixed clay positions
# EQ_NpT_F - equilibration in NpT ensemble and fixed clay positions
# EQ_NVT - equilibration in NVT ensemble
# EQ_NpT - equilibration in NpT ensemble
# D-SPACE - d-spacing equilibration
# (any other name) - production run

# Example for run tyes with specifications:
# SIMINP:
#  EM:
#     FREEZE_CLAY: True # clay positions are kept fixed
#                       # (optional parameter, default: True)
#  EQ_NVT_F or EQ_NpT_F:
#      NSTEPS: 1000 # number of steps
#  EQ_NVT or EQ_NpT:
#      NSTEPS: 1000 # number of steps
#  D-SPACE:
#      D_SPACE: 15.0 # target d-spacing in angstrom
#      NSTEPS: 1000 # timesteps between interlayer water removal
#      Options for specifying number of removed waters (select ONE!):
#      1. Absolute number of water molecules per interlayer space
#      SHEET_WAT = 2
#      2. Number of water molecules per unit cell
#      UC_WAT = 0.1
#      CONDA_ENV: ClayCode # optional conda environment for d-spacing equilibration run
#      SHELL: bash # optional shell for d-spacing equilibration run
#  P:
#      NSTEPS: 100000 # number of steps
#  P_1:
#      NSTEPS: 200000 # number of steps

SIMINP:
  EQ_NVT_F:
    NSTEPS: 1000000
    FREEZE:
      - clay
  EQ_NpT:
    NSTEPS: 1000000

# =============================================================================
# Path specifications
# =============================================================================

# Minimal required specifications:
# 1. Absolute or relative location of coordinate and topology files
# INPUT and/or OUTPUT: (if only one is given, these will be identical)
#   -> ClayCode will look for most recent GRO and TOP file inside directory
# INPATH: '/storage/clay_models'
# OUTPATH: '/storage/clay_models'

INPATH: '/path/to/input/directory'
OUTPATH: '/path/to/output/directory'
RUN_PATH: '/path/to/run/directory'

# 2. Manually specifies absolute or relative paths of input GRO and TOP files
# if none of the options from 1. are given, output files will be placed inside
# parent directory of GRO, if a checkpoint CPT file with the same path and
# namestem as INGRO is found, it will be used as input for the simulation run
INGRO: 'file_name.gro'
INTOP: 'file_name.top'

# Template file for run script
# If not given, run commands will be written to an empty shell script file.
# RUN_SCRIPT: '/path/to/template/file.sh'
RUN_SCRIPT: '/path/to/script.sh'

# Specify a shell for the run script (default: bash)
#SHELL: bash

# =============================================================================
# Optional: Simulation Runs Specifications
# =============================================================================

# Manually override default MDP options for all (MDP_PRMS)
# or specific run types (RUN_PRMS)
# MDP_PRMS: '/path/to/mdp/file.mdp'
# RUN_PRMS:
#   EQ_NVT_R: '/path/to/new/EQ_NVT_R/mdp/file.mdp'
#   P_1: '/path/to/new/P_1/mdp/file.mdp'

MDP_PRMS: '/path/to/mdp/file.mdp'
RUN_PRMS:
#  EM: '/media/hannahpollak/free/test_cc/IMt_1/em.mdp'
  EQ_NVT: '/path/to/nvt_mdp/file.mdp'
  EQ_NpT: '/path/to/npt_mdp/file.mdp'
  D_SPACE: '/path/to/d_spacing_mdp/file.mdp'
  ctl: '/path/to/production_run_mdp/file.mdp'



# -----------------------------------------------------------------------------
# bash alias for used GROMACS version
# -----------------------------------------------------------------------------

# bash alias or path of GROMACS executable (default: gmx)
GMX: gmx

# GROMACS version (specify if different from local GROMACS installation)
GMX_VERSION: 

# =============================================================================
# Required Parameters
# =============================================================================

# name of system to call according to CLAY_COMP
SYSNAME: