Tristan BEREAU, University of Basel, 2013
Perform thermodynamic integration of gas-phase and solvated compounds in CHARMM.
Clone the main repository
git clone [email protected]:tbereau/charmm.ti.git
go to the charmm.ti
directory (which we'll call $DIR
). It contains an empty directory briz
,
which needs to be cloned independently
git clone [email protected]:tbereau/briz.git
When using any of the scripts, do not copy them away from the original directory, as some files rely on one another. Instead, either call them from their absolute path or use symbolic links.
the perform-ti
script generates, runs/submits, and analyzes thermodynamic
integration (TI) simulations with CHARMM.
$DIR/perform-ti [-h] --ti {vdw,pc,mtp} [--chm CHARMM] --tps TPS [--top TOP]
--par PAR --slu SLU [--slv SLV] [--lpun LPUN]
[--lmb LMB LMB LMB] [--nst NSTEPS] [--neq NEQUIL]
[--rem REMOTE] [--num NUMPROC] [--sub] [--dir SUBDIR]
[--back] [--dual DUAL DUAL DUAL]
Options:
-h help
-ti {vdw,pc,mtp} interactions to couple: van der Waals, point charges, or multipoles
--chm CHARMM location of the CHARMM executable on local machine
--tps TPS topology of solute molecule (required)
--top TOP optional topology file (can call option multiple times)
--par PAR parameter file (>=1x required; can call option multiple times)
--slu SLU solute PDB file
--slv SLV solvent PDB file (only for liquid simulations)
--lpun LPUN local PUN file for multipole simulations
--lmb LMB LMB LMB lambda spacing: START, SPACING, END (default: 0.0, 0.1, 1.0)
--nst NSTEPS total number of steps per simulation (includes equilibration)
--neq NEQUIL number of steps for equilibration
--rem REMOTE name of remote cluster
--num NUMPROC number of cores per simulation
--sub submit simulations and exit the script (otherwise the script waits)
--dir SUBDIR name of the SUBDIR on the remote cluster; useful to restart runs
--back backward simulations
--dual ML1 ML2 DUA dual topology: provide molecular names of MOL1, MOL2, and DUAL (work in progress)
The script will generate all CHARMM input files to run TI using the selected lambda spacings.
The --rem
option allows to submit all jobs to a remote cluster. The script then waits for
all simulations to complete, gathers the data back to the local machine, and exits the script.
Note that this option requires the configuration of the hosts.ini
file in the $DIR/briz
directory.
To do so, copy $DIR/briz/hosts-sample.ini
to $DIR/briz/hosts.ini
and adapt it to your needs.
The --lpun
option, coupled with --ti mtp
will generate CHARMM input files for multipole simulation,
using the MTPL module (coming to a future release of CHARMM; please email me for details).
The generate-solvated-box
solvates a single molecule in a box of water and equilibrates the
box using CHARMM and VMD.
$DIR/generate-solvated-box file.top file.pdb file.par
where
file.top topology file of the solute molecule
file.pdb PDB file of the solute molecule
file.par parameter file of the solute molecule
This script is a simple wrapper for perform-ti
that runs all pc
, mtp
, and vdw
TI simulations. See script for details.
Parses output log file of a perform-ti
run and extracts the free energy of each lambda
window. See script for more details.
Reads out and display all free energies for forward and backward simulations in both vacuum
and water. The script requires the presence of pc
, mtp
, and vdw
contributions.
See script for more details.