Tutorial-l Mailing List

From: Robert Coffman (robertcoffman12_at_gmail.com)
Date: Tue May 03 2022 - 19:48:04 CDT

Ribi,

The "firsttimestep" command is not as important as it sounds. I have
noticed in my own simulations that if I leave that command out of the input
file, the restarted simulation just starts counting steps at 1 again (but
not actually starting over). It is a neat method to keep track of how many
timesteps have passed in the output files but does not actually determine
where the next restart starts. In other terms when a simulation is
restarted from the .coor, .vel and .xst files it always starts where those
ended and cannot go back to a previous steps velocities by simply
designating "firsttimestep 900" when the last run ended at 1000. (as far as
I know, Any correction on this point is welcome)

Using 0 as the firsttimestep is the same as leaving that command out of the
input file entirely.

I hope this helps.

Sincerely,

Robert Coffman
PhD Candidate
Brigham Young University

ps. If you want to start the simulation at some arbitrary time point you
sort of can. It would require that the coordinates were captured for that
time in the DCD output file and then you would save them as a new .pdb
file. You would have to use the .xst file (find the same timestep in the
file) or vmd to measure the system size and either restate the system size
in the input file or manually edit the .xsc input file with the correct
dimensions. One big caveat is that I do not know how to restart from that
arbitrary point with the same velocities that those atoms had at that time.
The system would be reassigned new velocities at startup.

On Tue, May 3, 2022 at 10:38 AM Ribi Akbar <ra.ribiakbar_at_gmail.com> wrote:

> Hi,
>
> I have a question regarding the use of the command "firsttimestep". This
> command is particularly important when restarting a simulation. However, in
> the input file we include the information from the previous simulation
> (.coor .vel and .xst). Assuming that our simulation stopped working at 1000
> timestep, what could happen if we specify the firsttimestep as 900 instead
> of 1100 or 1000 (say)?
> And also what if we just use 0 as the first time step?
>
> Thank you
>

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