Hi,
Yes. You can do your correlation function in step numbers and scale those
when you produce output.
Mark
On Wed., 19 Jun. 2019, 19:53 Eric R Beyerle, wrote:
> I'm calculating a time correlation function from the trajectory using an
> in-house code and I wanted to make sure the timesteps
I'm calculating a time correlation function from the trajectory using an
in-house code and I wanted to make sure the timesteps between each frame
are the same (i.e. the 0.2 ps write interval specified in the .mdp
file). Based on your response, it seems as though they are.
Many thanks,
Eric
Hi,
The simulation is 100% fine. Many of the tools (and their implementations)
date from earlier eras where so many time steps were simply impossible, and
some of what they do with handling time (as a floating-point number)
doesn't work well. Once you have about 7 significant digits in the time
Hi,
I've run a fairly long (1 microsecond) trajectory of ubiquitin in spc/e
on a supercomputer that allows a 48-hour runtime on their nodes. Since
the simulation doesn't finish in 48 hours, I used the checkpoint files
from the simulation to restart the simulation, using the following mdrun
