Re: A serious problem of NAMD output.

From: Peter Freddolino (
Date: Tue Jul 24 2007 - 18:57:42 CDT

This appears to have been a cutoff issue; the atoms flew apart and there
were no long range electrostatics in the configuration being used.

Brian Bennion wrote:
> Hello,
> 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.
> regards
> Brian
> 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.
>> Thanks.
>> Boyang.

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