From: Himanshu Khandelia (hkhandel_at_dtc.umn.edu)
Date: Wed Mar 22 2006 - 16:45:17 CST
Thank you all for your replies. Please do correct me if I am wrong:
after the first 89000 steps of equilibration, I can run 1 ns (say) of
simulation, in 20 increments of 50 ps each, using the .vel, .coor and the
.xsc outpup from the previous 50 ps simulation. In this case, I will not
need to specify firsttimestep, unless one of these simulations crashes,
and I need to use the restart file, right?
Also, I am using Langevin dynamics, but the simulations are being run on a
single processor.
thanks !
-Himanshu
On Wed, 22 Mar 2006, snoze pa wrote:
> 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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