[gmx-users] Run time for energy minimization, nvt, and npt equilibration

Thanh Le thanh.q.le at sjsu.edu
Mon Aug 1 22:47:30 CEST 2016

Hi guys, I have a question regarding the run time for energy minimization,
nvt and npt equilibration steps. Currently, I am doing a RNA-protein
simulation (using ff amber14 and spce water model) in a 10 A octahedron box
containing almost 400k solute atoms.
For the energy minimization step, I did it for 2 ns and received a
potential E of nearly -2.25e-7.
I am also doing 2ns for nvt and npt equilibration steps.
My question is: is 2ns too long for these steps?
Also another question regarding running simulation on a cluster: do I need
to install gromacs mpi to run it on parallel? Is it necessary since I read
in the literature gromacs would use all the available cores to run if I
dont specify the number of cores.
Thanh Le

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