Periodic cel too small

From: Alemayehu Gorfe Abebe (
Date: Tue Jan 13 2004 - 08:33:39 CST

Dear NAMD users,

I recently started using NAMD for simulations. After successfull runs of
several systems, I encounted the following error in one case.

"FATAL ERROR: Periodic cell has become too small for original patch
Possible solutions are to restart from a recent checkpoint,
increase margin, or disable useFlexibleCell for liquid simulation."


I tried several things, but with no success. I used the same setup as in
my other simulations and all work fine with or thithout PME. Besides,
the same system runs fine with CHARMM

(I use CHARMM for setup and equilibration in all cases, only because I
am more familiar with it, and I had no problem reading in a psf (xplor
format) and pdb into NAMD and do the production phase with NAMD).

Has anybody experienced this before? What would be the problem? I note
again that the same system runs just fine in CHARMM and I therefore
doubt that it is a problem of setup/equilibration.

Thanks in advance!

A. Abebe

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