From: Nitin Bhardwaj (
Date: Fri Jan 05 2007 - 12:31:18 CST

Dear Namd users,
     I have a strange problem in my simulation of a single lipid
molecule. During minimization, I keep getting this warning "Not all atoms
have unique coordinates". The simulation stops as soon as production run
starts with the message:

Reason: 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 increasing the magint but no help. I check my molecule and
everything is fine with it. There are no atoms overlapping.

Its NAMD2.6 on linux.

Has anyone seen this problem before? Is there any way to go around this?

Thanks a lot in advance.