AW: Keep PBC box size in Z-direction constant?

From: Norman Geist (
Date: Tue Feb 21 2012 - 00:27:45 CST


You can hold it only in XY with "useconstantarea", so you could simply rotate your box and let pressure happen in Z. The reason why your simulation crashes might be fixed atoms at the boundaries of the periodic box, which cannot be rescaled or something very similar. Often this error comes with fixed atoms. You could try to increase the relaxation time of the pressure control if you do not have fixed atoms at the boundaries, but inside the system, as sometimes it happens that the atom coordinate rescaling due to pressure, when happening in too big step, creates heavy forces when rescaling free atoms into fixed ones.

Feel free to ask further.

Good luck

Norman Geist.

> -----Ursprüngliche Nachricht-----
> Von: [] Im
> Auftrag von Bjoern Olausson
> Gesendet: Montag, 20. Februar 2012 13:37
> An:
> Betreff: namd-l: Keep PBC box size in Z-direction constant?
> Hi NAMD users,
> is it possible to keep the PBC-Box size in the Z-direction fixed?
> I am asking because I want to run a NPT simulation in which the box
> size is not allowed to shrink/extend along the Z-axis.
> I tried to disable useFlexibleCell but after a few nanoseconds the
> simulation crashes with the message "FATAL ERROR: Periodic cell has
> become too small for original patch grid! ..."
> To work around this I decreased the number of steps after which I
> restart the simulation from a checkpoint to 5000ps and increased the
> margin. But nothing helps. After 1.5ns the simulation just keeps
> crashing no matter how small I set the individual run or how large I
> choose the margin.
> So is there a way to allow fluctuations along X any Y and keep Z rigid
> or any other workaround to prevent the above error?
> Cheers,
> Bjoern

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