mdpow scripts

A simple, shell-based workflow uses the mdpow scripts. These scripts are all named mdpow-COMMAND and are installed with the MDPOW package. Each script has a usage that can be obtained with mdpow-COMMAND --help.

Input files

You need

• ITP file
• structure file (PDB or GRO)

Workflow

Initial setup

Create a working directory and put the input files into the working dir, e.g.

mkdir benzene && cd benzene
cp ~/src/MDPOW/doc/examples/benzene/benzene.{itp,pdb}  .

(assuming that the checked out MDPOW sources are in ~/src/MDPOW to get these example files).

Create a run input file. The following will work once #74 is fixed:

mdpow-get-runinput runinput.yml

(until the bug is fixed: cp ~/src/MDPOW/mdpow/templates/runinput.yml .)

Edit runinput.yml and adjust the name, itp, and structure file. Change the run times. If you have a specific template scripts for your queuing system, add it to the directory and add it to the runinput file. A minimal Gridengine script would be

# Gridengine script for MDPOW: 'mdpow.ge'
#$ -S /bin/bash
#$ -N MDPOW
#$ -cwd -j y -R y -r n
# more resource requests eg for parallel environment
TPR='md.tpr'
DEFFNM=md
# get Gromacs environment (specific to site)
module load gromacs/4.6.6/cuda5/intel13.0/avx/bare/64
mdrun -nt $NSLOTS -s $TPR -deffnm $DEFFNM -c $DEFFNM.pdb -cpi

Load the gromacs environment, for example by sourcing GMXRC or via a module command

module load gromacs/4.6.6/cuda5/intel13.0/avx/bare/64

Equilibrium MD

Create run files for the NPT equilibration of the small molecule in water:

mdpow-equilibrium --solvent water runinput.yml

This will run Gromacs for some of the steps locally (see runinput file). It will create a directory NAME/Equilibrium/water/MD_NPT/ where NAME is the name of the compound as supplied in the runinput file. The directory contains all the files needed to start a Gromacs job and also a queuing system script file (if a template was provided; in the following I assume that this is the case and that the script is called mdpow.ge):

Submit the MD job:

cd NAME/Equilibrium/water/MD_NPT/
qsub mdpow.ge

FEP MD

Once the NPT MD has completed, set up the alchemical free energy calculations:

mdpow-fep runinput.yml

This will create one directory for each FEP window. One can launch all jobs with

cd NAME/FEP/water/
for d in {Coulomb,VDW}/????; do (cd $d && qsub mdpow.ge); done

Analysis

Collect the data and compute the solvation free energy

mdpow-solvationenergy --solvent water NAME

By default, the data are appended to a file gsolv.txt; for more options, see mdpow-solvationenergy --help.