From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Thu Mar 10 2016 - 01:05:33 CST
We need to see your full input script, since it looks you're doing npt?
Norman Geist
> -----Ursprüngliche Nachricht-----
> Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im
> Auftrag von Olya Kravchenko
> Gesendet: Donnerstag, 10. März 2016 04:23
> An: NAMD <namd-l_at_ks.uiuc.edu>
> Betreff: namd-l: periodic boundary condition in XY, hard wall in Z - errors
>
> Hi all,
>
> I would like to apply periodic boundary conditions only in X and Y
> directions. In my config file I used the following entry:
>
> # Periodic Boundary Conditions
> cellBasisVector1 70.0 0. 0.0
> cellBasisVector2 0.0 70.0 0.0
> cellBasisVector3 0.0 0 0.0
> cellOrigin 30.0 30.0 32.5
>
> wrapAll on
> margin 5
>
>
> When I submit the job it runs for a while until I see the following error:
>
> WRITING COORDINATES TO DCD FILE ar_force_out.dcd AT STEP 20750
> FATAL ERROR: Periodic cell has become too small for original patch grid!
> Possible solutions are to restart from a recent checkpoint,
> increase margin, or disable useFlexibleCell for liquid simulation.
>
> How can I address this error? Is this the right way to set up PBC in 2
> dimensions?
>
> My simulation cell is actually around (~61 ~61 ~62), as measured by
> minmax. I played with numbers and noticed that my simulation runs
> longer if I increase both the margin and cell basis vectors.
>
> I saw some of the older threads in the archives where the margin was
> discussed but it's not clear how large should it be. If I want to run
> my simulation for 500 000 steps, what margin should I set up?
>
> Also, when choosing cell basis vector, how much bigger should it be
> than what is measured by "measure minmax"?
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