Re: A serious problem of NAMD output.

From: Brian Bennion (
Date: Tue Jul 24 2007 - 18:43:05 CDT


 From your psf file I can see that the CT and CA labels might be
reversed. Also, how far apart are the atoms. You did not include a
pdb file that had coordinates or a log file.
The psf file shows that the atoms are in the same residue. This is
far fetched, but if namd does read these two as being in the same
residue it will not calculate electrostatics based on the 1/4 exclusion rule.


At 03:35 PM 7/24/2007, Wang, Boyang wrote:
>Dear all,
>when I run the simulation of two charged atoms, I see that the output of
>electrostatic energy is 0.
>I am very confused and I appreciate that you would help me with this
>problem using the attached simulation files.

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