Re: "Not all atoms have unique coordinates"

From: Neelanjana Sengupta (
Date: Fri Jan 05 2007 - 13:16:40 CST

It looks like you have some bad contacts between atoms, which remain even
after minimization. Did the "production run" go forward by even a few steps?
If so, you can try re-starting the simulation from wherever it
stops...sometimes that solves the problem.
Otherwise, you may have to re-check your starting conformations.


On 1/5/07, 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

Neelanjana Sengupta, PhD student
Dept. of Chemistry
Univ. of California-Irvine
Irvine, CA 92697
Phone: 1-949-824 9921

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:44:17 CST