Re: "Not all atoms have unique coordinates"

From: Marcos Sotomayor (
Date: Fri Jan 05 2007 - 13:39:17 CST

Hi Nitin,

Very likely your psf and/or pdb files have some error. You should NOT have
a "Not all atoms have unique coordinates" message.

How are you setting up periodic boundary conditions for a single lipid


On Fri, 5 Jan 2007, Nitin Bhardwaj wrote:

> 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
> grid!
> 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.
> Rgds,
> Nitin

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