SimpleRun Flow

The SimpleRun Flow is a straightforward pipeline that allows performing simple Molecular Dynamics (MD) simulations. Before running a productive MD simulation, an equilibration phase comes first and the length is automatically obtained from the productive simulation time.

At the beginning of the equilibration, 500 steps of 4fs in a NVT ensemble are performed and then NPT is applied. During this stage, several constraints are applied to protein atoms and progressively reduce to be zero.

SimpleRun flow can submit the simulations not only directly to the Local GPUs, but also with LSF and Slurm queues. Furthermore, the SimpleRun flow allows to set up a ‘flat bottom potential’ when a membrane system is provided. This feature avoids that a particular molecule (in this case the ligand) can cross the box from the extra cytosolic to cytosolic environment due the periodic boundary conditions.

Usage

Examples

Get the data for running the SimpleRun Flow examples here. Unzip and untar it and follow the next examples.

There, two build folders can be found: build_amber and build_charmm.

Run a simulation of a globular system (built in Amber)

To run a simple MD simulation for a protein globular (non-membrane) system, one can use the following command:

aceflow SimpleRun --inputdirs simplerun/build_amber --simplerundir test_globular --runtime 1 --memb False --execmode Local

Run a simulation of a membrane system (built in CHARMM)

To run a simple MD simulation for a protein-membrane system with a ligand named MOL in the outer-membrane environment, one can use the following command:

aceflow SimpleRun --inputdirs simplerun/build_charmm --simplerundir test_membrane --runtime 1 --memb True --memblig MOL --execmode Local