From: snoze pa (snoze.pa_at_gmail.com)
Date: Wed Mar 22 2006 - 16:24:49 CST
But if you want to restart you job the you should use
firsttimestep(lasttimestep here).
On 3/22/06, Marcos Sotomayor <sotomayo_at_ks.uiuc.edu> wrote:
>
> As Sterling mentioned, the firsttimstep parameter is just a label, only
> useful for SMD simulations (as far as I know).
>
> Note that if you are using Langevin dynamics (are you?), energies and
> coordinates will never be the same since *random* forces are applied
> (unless you use the same seed). If you are running in parallel, you may
> also have roundoff errors, but that should be minor, noticeable only after
> many time steps....
>
> Marcos.
>
> On Wed, 22 Mar 2006, Sterling Paramore wrote:
>
> > 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.
> >
> > -Sterling
> >
> > Himanshu Khandelia wrote:
> >
> >> Hello,
> >>
> >> 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
> >> errors.
> >>
> >> HELP !
> >>
> >> -Himanshu
> >>
> >
>
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