From: Jacqueline Schmidt (jacqueline_schmidt_1983_at_yahoo.com)
Date: Tue Aug 28 2012 - 19:17:54 CDT
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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