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Running gmx_MMPBSA

Before running gmx_MMPBSA

gmx_MMPBSA requires minimal preprocessing of the input structure and trajectory files. Before running gmx_MMPBSA, complete the following checks.

Check the structure supplied with -cs, -rs, or -ls

Visualize the structure contained in the structure input file given in the -cs, -rs, or -ls options and make sure it is intact and centered (Figure 1, right). A "broken" structure (Figure 1, left) can produce inconsistent results.

Generate the structure from a *.tpr file:

gmx editconf -f md.tpr -o md.pdb

overview
Figure 1. Visualization of two input structure files. Left: "broken" structure; right: centered structure

Remove PBC artifacts from trajectories supplied with -ct, -rt, or -lt

Visualize the trajectory supplied with -ct, -rt, or -lt and make sure periodic-boundary artifacts have been removed (Figure 2, right). An unfitted or broken trajectory (Figure 2, left) can produce inconsistent results.

Steps:

  1. Generate a group that contains both molecules

    gmx make_ndx -n index.ndx

>1 | 12

>q

    Assuming 1 is the receptor and 12 is the ligand. This creates a new group (number 20 in this example)

  2. Remove PBC artifacts

    gmx trjconv -s md.tpr -f md.xtc -o md_noPBC.xtc -pbc mol -center -n -ur compact
center: 20 (created group)
output: 0

  3. Remove rotation and translation relative to the reference structure (optional)

    gmx trjconv -s md.tpr -f md_noPBC.xtc -o md_fit.xtc -n -fit rot+trans
fit: 20 (created group)
output: 0

  4. Inspect the processed trajectory

    Make sure that the trajectory is intact and centered (Figure 2, right).

  5. If the process is unsuccessful, consider another option such as -pbc nojump (as suggested here).

overview
Figure 2. Visualization of two input trajectories. Left: trajectory with PBC artifacts; right: centered and fitted trajectory with PBC artifacts removed.

Running gmx_MMPBSA

Tip

  • Since version 1.4.0 we have fixed the gmx_MMPBSA inconsistencies when using MPI.
  • We currently recommend the use of MPI since the computation time decreases considerably.

Like MMPBSA.py, gmx_MMPBSA uses MPI only for the energy calculations. The remaining steps —such as generating or converting Amber topologies, preparing mutations, and dividing trajectories— run in a single thread (see Figure 3). AmberTools and GROMACS therefore do not need to be compiled with MPI support. The preprocessing time depends on the system and is the same for serial and MPI runs.

Note

Note that gmx_MMPBSA processes, converts, or builds topologies from GROMACS files, so it takes slightly longer than MMPBSA.py at the same stage of the process. However, this is not really significant.

Remember

Make sure that you install the OpenMPI library

sudo apt install openmpi-bin libopenmpi-dev openssh-client

A usage example is shown below:

mpirun -np 2 gmx_MMPBSA -O -i mmpbsa.in -cs com.tpr -ci index.ndx -cg 1 13 -ct com_traj.xtc

#!/bin/sh
#PBS -N nmode
#PBS -o nmode.out
#PBS -e nmode.err
#PBS -m abe
#PBS -M email@domain.edu
#PBS -q brute
#PBS -l nodes=1:surg:ppn=3
#PBS -l pmem=1450mb or > 5gb for nmode calculation

cd $PBS_O_WORKDIR

mpirun -np 3 gmx_MMPBSA -O -i mmpbsa.in -cs com.tpr -ci index.ndx -cg 1 13 -ct com_traj.xtc > progress.log

Danger

When running gmx_MMPBSA with MPI, do not use the GROMACS gmx_mpi executable because it can conflict with mpirun. Use gmx instead. Only mdrun benefits from GROMACS MPI parallelization; the GROMACS tools called by gmx_MMPBSA run in a single thread. See issue 26 for an example.

Warning

The nmode calculations require a considerable amount of RAM. Consider that the total amount of RAM will be:

RAMtotal = RAM1_frame * NUM of Threads

If it consumes all the RAM of the system it can cause crashes, instability or system shutdown!

Note

At a certain level, running RISM in parallel may actually hurt performance, since previous solutions are used as an initial guess for the next frame, hastening convergence. Running in parallel loses this advantage. Also, due to the overhead involved in which each thread is required to load every topology file when calculating energies, parallel scaling will begin to fall off as the number of threads reaches the number of frames.

This version is installed via pip as described above. AMBERHOME variable must be set, or it will quit with an error. An example command-line call is shown below:

gmx_MMPBSA -O -i mmpbsa.in -cs com.tpr -ci index.ndx -cg 1 13 -ct com_traj.xtc

You can find test files on GitHub.

drawing

Figure 3. MPI benchmark description from MMPBSA.py paper. MMPBSA.py scaling comparison for MM-PBSA and MM-GBSA calculations on 200 frames of a 5910-atom complex. Times shown are the times required for the calculation to finish. Note that MM-GBSA calculations are ∼5 times faster than MM-PBSA calculations. All calculations were performed on NICS Keeneland (2 Intel Westmere 6-core CPUs per node, QDR infiniband interconnect)

Last update: August 29, 2026 16:48:15
Created: January 27, 2022 07:53:46
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