g_mmpbsa

Executing g_mmpbsa

g_mmpbsa is a console application which is executed from terminal/console by command options similar to other GROMACS module. 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.

To get extensive details of usage with options, please click on Usage.

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

g_mmpbsa -f traj.xtc -s topol.tpr -n index.ndx -mme -mm energy_MM.xvg -decomp -mmcon contrib_MM.dat

Only polar solvation energy with energy decomposition

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

An example mmpbsa.mdp is provided in g_mmpbsa/test/polar_orig.

Only non-polar solvation energy with energy decomposition

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

• An example mmpbsa.mdp for SASA model is provided in g_mmpbsa/test/sasa_orig.
• An example mmpbsa.mdp for SAV model is provided in g_mmpbsa/test/sav_orig.
• An example mmpbsa.mdp for WCA model is provided in g_mmpbsa/test/wca_orig.

All energetic term with energy decomposition

g_mmpbsa -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 

NOTE: Please monitor the RAM because combined Molecular-Mechanics and Polar-Solvation energy calculation may require GBs of memory.

Using g_mmpbsa with external APBS

When g_mmpbsa is compiled and installed without linking with APBS libraries, an external APBS executable could be used. An environment variable $APBS should be defined for path to APBS executable before using g_mmpbsa.

export APBS=/usr/local/bin/apbs

Parallel computation using OpenMP

g_mmpbsa inherits OpenMP parallel comuputation implemented in APBS 1.2.x, 1.3.x and 1.4.x. 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.

Parallel computation using mpirun

Although g_mmpbsa does not support mpirun, it can use external APBS with mpirun. This external APBS should be compiled and linked against MPI. Environment variable $APBS should be defined before executing g_mmpbsa. For example:

export APBS="mpirun -np 8 apbs"

Afterwards, g_mmpbsa uses this apbs with mpirun, and calculates polar-solvation energy using 8 processors.

Note: Presently, MPI support in APBS-1.4.1 is broken, therefore, only use APBS-1.3.x versions.