From: Sterling Paramore (paramore_at_hec.utah.edu)
Date: Wed Mar 22 2006 - 15:40:02 CST
The firsttimestep parameter is totally irrelevant for most things done
in NAMD and does not affect subsequent calculation (SMD would be an
exception). It's just a way to label the timesteps as you see
appropriate. Usually, you'll want it to refer to the timestep of the
restart file. In your example, you might want to set it to 89000, as
your new trajectory is supposed to be a continuation of the equilibration.
You're probably getting different energies and coordinates because NAMD
trajectories over multiple processors are not reproducible. As I
understand it, this is because with mutliple processors, numbers are
added up in different orders depending on what processor gets what part
of the simulation. This changes the roundoff error between trajectories
which very quickly leads to divergence.
Also, catdcd does not read the timesteps, only the frames.
Himanshu Khandelia wrote:
>I have been totally baffled with the firsttimestep parameter, and its
>meaning. I ran an equiliration run for 89000 steps. I then started a
>dynamics run, as a continuation of equilibration, varying the
>firsttimestep parameter as follows:
>Case 1: firsttimestep 0
>Case 2: firsttimestep 89000
>Case 3: firstimestep 89020 (20 was the stepspercycle parameter)
>Case 4: I did not define the firsttimestep parameter
>In EACH of the above cases, I get different energies and coordinates.
>Which one is the correct value to use, and why ? Also, in each case,
>"catdcd" merges the dcd files from equilibration and dynamics without any
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