[gmx-users] Timestep in GROMACS simulation

Kevin Boyd kevin.boyd at uconn.edu
Wed May 29 02:43:47 CEST 2019


That totally depends on your forcefield. Most classical all-atom
forcefields are recommended to be run with a 2 femtosecond timestep.
Some coarse-grained forcefields like Martini can do 20+ fs, but you’ll
want to check the literature.

As for better sampling, you simply sample longer times for the same
number of steps. There's no real per-step performance penalty for
increasing the timestep, so if each step you take is 10x longer, and
you have the same number of steps, you've simulated 10x more time.



> On May 28, 2019, at 8:35 PM, Anh Vo <atv55 at msstate.edu> wrote:
> Hi all,
> How did you choose your timestep and simulation time when running GROMACS?
> Is there any logic for deciding that?
> I’ve read that larger time step permits better sampling without significant
> errors in observed thermodynamic, structural or dynamic properties => What
> does “sampling” mean? Why does the larger time step allow better sampling?
> Thank you a lot.
> Best,
> Anh Vo
> --
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