Setup config.ini file

Most scripts rely on a set of user-defined variables that help define paths to executables, as well as connections to remote clusters. Copy the file src/config-sample.ini to src/config.ini. It consists of three sections (see below for details):

1. local configuration
2. remote configuration for ab initio calculations
3. remote configuration for liquid simulations

:::ini
; Paths for executables on local machine
[local]
charmrun  = '/home/bereau/soft/charmrun'
namd      = '/home/bereau/soft/namd2'
charmm    = '/home/bereau/soft/charmm'

; Paths for remote cluster to run ab initio calculations
[remote]
hostname  = 'maia.urz.unibas.ch'
user      = 'bereau'
workdir   = '/home/chemie/bereau/notsaved/remote'
gsub      = '/home/chemie/bereau/save/soft/gsub'
gaussext  = 'inp'
gaussout  = 'out'

; Paths for remote cluster to run liquid simulations
[remliq]
hostname  = 'beethoven.chemie.unibas.ch'
user      = 'bereau'
workdir   = '/home/bereau/data/remote'
charmmsub = '/home/bereau/bin/charmmsub'
charmmout = 'out'
ncpu      = 4

• charmrun, namd,charmm` must point to the absolute paths of the executables.
• hostname and user provide the address of the remote cluster. Note that the ssh connection must happen without the need for the password. See, e.g., this link for details.
• workdir is the directory in which the script will place temporary files. Make sure this directory exists when running any script.
• gaussext and gaussout are the input and output files that the Gaussian calculation will provide, respectively (e.g., .inp and .log).
• Similarly, charmmout is the extension of the CHARMM output files.
• ncpu is the number of cores requested per liquid simulation.