[gmx-users] Timestep in GROMACS simulation

[Anh Vo]

Hi,

I'm still not clear what "sampling" means. Does it mean collecting data
from the simulation?

Thank you very much for your answer.

Best,
Anh Vo


  -----Original Message-----
>
>
> Message: 4
>
> Date: Tue, 28 May 2019 20:43:32 -0400
>
> From: Kevin Boyd <kevin.boyd at uconn.edu>
>
>
>
> Hi,
>
>
>
> 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.
>
>
>
> Kevin
>
>
>
> Kevin
>
>
>
> > 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
>
>
>