Getteing started with MM/PBSA calculation

g_mmpbsa command contains several sub-commands. The main command to run MM/PBSA calculation is g_mmpbsa run. All the input options should be provided on command line depending on the type of calculation. To calculate for single atomic group (e.g. only protein, only ligand, only specific region of protein etc.) one group is required to choose from index file, whereas for complex (e.g. protein-ligand, protein-protein etc.) two separate group is required to choose from index file.

For more details about g_mmpbsa run command, visit usage or type following command:

g_mmpbsa run -h

Warning

On MacOS, external APBS is required to run this command. If APBS is not installed, the command will fail with an error message.

Use Homebrew to install APBS on MacOS (brew install brewsci/bio/apbs).
Define APBS environment variable to point to the APBS executable, e.g. export APBS=$(brew --prefix apbs)/bin/apbs.

Only molecular mechanics (vdw and electrostatic) vacuum energy with energy decomposition

g_mmpbsa run -f traj.xtc -s topol.tpr -n index.ndx -unit1 Protein -unit2 Ligand \
             -mme -mm energy_MM.xvg -decomp -mmcon contrib_MM.dat

Here traj.xtc is the trajectory file, topol.tpr is the topology file, index.ndx is the index file, Protein and Ligand are the group names of protein and ligand in the index file. energy_MM.xvg is the output file for MM energy and contrib_MM.dat is the output file for energy decomposition.

Only polar solvation energy with energy decomposition

g_mmpbsa run -f traj.xtc -s topol.tpr -i mmpbsa.mdp -n index.ndx \
             -unit1 Protein -unit2 Ligand -nomme -pbsa -decomp \
             -pol polar.xvg -pcon contrib_pol.dat

polar.xvg is the output file for polar-solvation energy and contrib_pol.dat is the output file for energy decomposition. An example mmpbsa.mdp file is provided.

Only non-polar solvation energy with energy decomposition

g_mmpbsa run -f traj.xtc -s topol.tpr -i mmpbsa.mdp -n index.ndx \
             -unit1 Protein -unit2 Ligand -nomme -pbsa -decomp \
             -apol apolar.xvg -apcon contrib_apol.dat

apolar.xvg is the output file for non-polar-solvation energy and contrib_apol.dat is the output file for energy decomposition.

An example mmpbsa.mdp file is provided for SASA only model.
An example mmpbsa.mdp file is provided for SAV only model.

All energetic term with energy decomposition

g_mmpbsa run -f traj.xtc            -s topol.tpr \
             -i mmpbsa.mdp          -n index.ndx -pbsa \
             -mm energy_MM.xvg      -pol polar.xvg \
             -apol apolar.xvg       -decomp \
             -mmcon contrib_MM.dat  -pcon contrib_pol.dat \
             -apcon contrib_apol.dat

Parallel computation using `OpenMP`

g_mmpbsa inherits OpenMP parallel computation implemented in APBS and also implement MM energy calculations in parallel. This parallel support is enabled by default and all processors/core will be used during runtime.

To control the usage of processors/cores, number of threads can be changed by defining environment variable. For example in bash, one can write following command:

export OMP_NUM_THREADS=X

where X is number of core/processors.

Warning

Not available on MacOS. APBS installed using Homebrew does not support OpenMP parallel computation on MacOS.

Getteing started with MM/PBSA calculation

Parallel computation using OpenMP

Parallel computation using `OpenMP`