Re: Warning: Not all atoms have unique coordinates.

From: Brian Bennion (brian_at_youkai.llnl.gov)
Date: Thu Jul 08 2004 - 11:06:08 CDT

Hi Shirley,

What did the psfgen ouput say when creating the psf and pdb files?

Have you checked them in VMD?

Also in regards to your cellbasis questions, they have to be a bit bigger
than the vmd minmax values or the periodic images will be so close to
each other that it may seen to namd that atoms are on top of each
other....

But the most common cause of this problem is a pdb file generated by
psfgen that has two atoms at 0.0 0.00 0.00
because psfgen could not parse the pdb and topology library appropriately.

Regards

Brian
On Thu, 8 Jul 2004, Shirley Hui wrote:

> I am trying to run a simulation on the L chain of the protein 1CPC (that is the pdb code). I "think" I have set everything up correctly, however, when I run the simulation there are some things that I am a bit concerned about:
>
> 1) I get a warning : Warning: Not all atoms have unique coordinates. (see second line of output below). This warning appears at each step in the console when the energies are outputted.
>
> 2) When I start the minimization process the energies values show up as 99999999.9999 (see output below). I believe this is because of the warning above.
>
> TCL: Minimizing for 500 steps
> Warning: Not all atoms have unique coordinates.
> PRESSURE: 0 8.41609e+22 -7.12353e+19 -2.98843e+20 -7.12353e+19 8.37347e+22 1.063
> 89e+20 -2.98843e+20 1.06389e+20 8.3925e+22
> GPRESSURE: 0 8.41609e+22 -7.12353e+19 -2.98843e+20 -7.12353e+19 8.37347e+22 1.06
> 389e+20 -2.98843e+20 1.06389e+20 8.3925e+22
> ETITLE: TS BOND ANGLE DIHED IMPRP
> ELECT VDW BOUNDARY MISC KINETIC
> TOTAL TEMP TOTAL2 TOTAL3 TEMPAVG
> PRESSURE GPRESSURE VOLUME PRESSAVG GPRESSAVG
>
> ENERGY: 0 966810.4900 404837.2614 2875.3521 77388.4504
> 99999999.9999 99999999.9999 0.0000 0.0000 0.0000
> 99999999.9999 0.0000 99999999.9999 99999999.9999 0.0000
> 99999999.9999 99999999.9999 13.1080 99999999.9999 99999999.9999
>
> So my question is why I am getting those warnings (that not all the atoms have unique coordinates?) This is obviously wrong but I wonder where I went wrong? Would it have been when I generated the PSF structure? Maybe my config file is wrong? I'm not really sure where to start to figure out what is wrong...
>
> I have attached my config file.
>
> thanks for any insight.
> shirley

*****************************************************************
**Brian Bennion, Ph.D. **
**Computational and Systems Biology Division **
**Biology and Biotechnology Research Program **
**Lawrence Livermore National Laboratory **
**P.O. Box 808, L-448 bennion1_at_llnl.gov **
**7000 East Avenue phone: (925) 422-5722 **
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