Re: Not all atoms have unique coordinates - revisited

From: Alberto Santana (
Date: Sat Oct 02 2004 - 08:32:59 CDT

Hi Brian,

>You didn't check the hydrated psf file and pdb file together did you?
I'm not quite sure what u mean here. I did check the pdb file carefully to
see if there were atoms with identical coordinates. I extracted all the
coordinates and ran a uniq -d command on it and no output, so NO two entries
were identical.

> Did you make your cell basis vectors insanely large just as a check?
I did change the cell basis vectors, but I did not change them by more than
5 or 6 units. I went from 78 to perhaps 83 or 84. The same to the other 2.
No more than that. Is it legal to change them insanely? I will make them
much bigger and try it again.

> Are all energies 999999 or is it bond, or angles or torsions?
No, just VDW, TOTAL, TOTAL2, and TOTAL3. I can send you the pdb/psf files if
this info is not enough.

OK, someone suggested a check of the pdb file and that it should not have
more than 99999 atoms. Ours have 6000 more than that but after the water is
added. An interesting point is that I compiled NAMD 2.5 on our cluster to
use Myrinet and also have the downloaded binary (NAMD_2.5b2ss03_Linux-i686).
The precompiled (downloaded binary) version RUNS NICELY without any
problems, no warning whatsoever, but the other one gives the warning and the
funny energies.


Alberto Santana, Ph.D.
Department of Chemistry
University of Puerto Rico - Mayaguez
P.O. Box 9019 Phone: (787) 832-4040 x3760
Mayaguez PR, 00681-9019

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:37:53 CST