AW: Warning: Not all atoms have unique coordinates

From: Norman Geist (
Date: Thu Aug 30 2012 - 01:54:20 CDT



if I were you, I would just check the pdb with vmd. Set the box with pbc set
{x y z} and possibly wrap to see if there are any overlapping atoms


Norman Geist.


Von: [] Im Auftrag
von Jacqueline Schmidt
Gesendet: Mittwoch, 29. August 2012 02:18
An: namd
Betreff: namd-l: Warning: Not all atoms have unique coordinates


Dear Namd users,

I have wrote a code to generate the pdb/psf files for surfaces (such as
clay) with periodicity (infinit surface in xy direction). I have checked the
energies at the zeroth step with lammps to make sure that my code works
fine. I get good agreements (less than 1 kcal/mol for bond and angle and
less than 5 for vdw and electrostatics). However, I get this warning
message: Warning: Not all atoms have unique coordinates. Is this mean that
there is something wrong in the pdb psf files? Because if two atoms are
superimposed the calculated energies must be infinity!! Is it possible that
the message is due to the periodicity of the surface atoms?


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