Prepare and check a molecular dynamics job
Run a small GROMACS water-box example, then inspect the input, trajectory and temperature.
Open the CEMP workflow
In AutoCompute, select Classical Molecular Dynamics and download the current system workbook. The example below reproduces the simulation stages with GROMACS 2018.8 using its built-in SPC water model. It does not depend on CEMP’s spreadsheet parameterization.
Run the downloadable example
Extract the archive into a new directory and run sh run.sh with GROMACS available. The script builds a 3 nm cubic box with 884 SPC water molecules, minimizes the energy, runs 10 ps of NVT at 298.15 K, then resumes from its checkpoint for 20 ps of NVT production. The time step is 2 fs and the trajectory is saved every 1 ps.
Inspect the outputs
Open reference/production.gro and reference/production.xtc together. gmx check reports 21 coordinate frames from 0 to 20 ps, including the initial frame. Read the temperature trace in reference/temperature.xvg. The recorded mean from the production energy file is 298.882 K. This short fixed-volume run demonstrates file handling and continuation. It does not establish equilibrium or converged material properties.
Example input or output
sh run.sh
gmx check -f production.xtc
# Reference: 2652 atoms, 21 coordinate frames, 1 ps between frames.