g_mmpbsa

De acordo com a página do 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.”.

Versões disponíveis

• g_mmpbsa/gromacs-5.1

Submissão de Jobs em Serial

Crie um arquivo chamado, por exemplo, submit_serial_jobs.sh.

#!/bin/bash
#SBATCH -t 24:00:00

export INPUT="traj.xtc topol.tpr mmpbsa.mdp polar.xvg apolar.xvg contrib_MM.dat contrib_pol.dat contrib_apol.dat"
export OUTPUT="*"

module load g_mmpbsa/gromacs-5.1

job-nanny 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

Para submeter o processo, basta usar o comando:

sbatch submit_serial_jobs.sh

Referências

Para informações adicionais sobre o software, consulte a documentação do g_mmpbsa.