Dear contributors, I am running gromacs simulations of Protein-Ligand complexes and calculating their binding affinity with the gmx_MMPBSA module. On a cluster, I have gmx_mpi, using which I parallelize my simulation runs, but gmx_MMPBSA does not work with gmx_mpi; hence it does not get parallelized and runs only on one core. The gmx_MMPBSA can be parallelized using the mpirun option, but it needs gmx for that, not gmx_mpi. So how to have both gmx and gmx_mpi on the cluster so that the simulation part uses gmx_mpi, while gmx_MMPBSA uses gmx, and this way, both could get parallelized?
Thanks in advance.
Rakesh Srivastava, Ph.D.
Dear contributors, I am running gromacs simulations of Protein-Ligand complexes and calculating their binding affinity with the gmx_MMPBSA module. On a cluster, I have gmx_mpi, using which I parallelize my simulation runs, but gmx_MMPBSA does not work with gmx_mpi; hence it does not get parallelized and runs only on one core. The gmx_MMPBSA can be parallelized using the mpirun option, but it needs gmx for that, not gmx_mpi. So how to have both gmx and gmx_mpi on the cluster so that the simulation part uses gmx_mpi, while gmx_MMPBSA uses gmx, and this way, both could get parallelized? Thanks in advance. Rakesh Srivastava, Ph.D.