How to determine minimum reasonable MD timing for ligand-protein complex

User discussions
1

I am working on protein-ligand complex MD simulation.
Now I’m running the tutorial.

gmx grompp -f md.mdp -c npt.gro -t npt.cpt -p topol.top -n index.ndx -o md_0_10.tpr

gmx mdrun -deffnm md_0_10

It use 10ns for md runs. The parameter is defined in it’s md.mdp file.

nsteps = 5000000 ; 2 * 5000000 = 10000 ps (10 ns)

It tooks 5 days to run with 16 cores CPU.
Is it normal?

Thus I seek a shorter time to execute.
What is the minimum reasonable time we can use? Is 1ns enough?

-Sca

2

The speed of the simulation depends on the quality of your hardware. Without careful benchmarking, there’s no way to say whether this is expected or not, but is in the ballpark of feasibility for an average laptop.

For the purposes of completing the tutorial, sure. For doing real science, absolutely not.

3

Thank you for your reply.