RE: "Not all atoms have unique coordinates"

From: Ana Celia Araujo Vila Verde (
Date: Fri Jan 05 2007 - 12:58:23 CST

Are you running NPT? I don't think you should, for a single molecule. you should run NVT (just comment out all the lines related to the pressure control in your configuration file for that). Also, make sure that cellBasisVectorX(Y,Z) is made 1) sufficiently bigger than your molecule, so that atoms from the original molecule don't overlap with atoms from the periodic image of the molecule and 2) bigger than your cutoff distance, so that the molecule does not interact with its image.
Let us know how it works.
Hope it helps,
Ana CÚlia Ara˙jo Vila Verde
Penn State University
Department of Chemical Engineering
Fenske Laboratory
University Park, PA 16802
Phone: +(1) (814) 863-2879
Fax: +(1) (814) 865-7846

-----Original Message-----
From: [] On Behalf Of Nitin Bhardwaj
Sent: Friday, January 05, 2007 1:31 PM
Subject: namd-l: "Not all atoms have unique coordinates"

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.

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