Re: Pair interaction : Energy values are zero

From: Eric H. Lee (
Date: Sun Jun 21 2009 - 16:23:43 CDT

This might seem a redundant question, but are your interacting
particles close enough to each other for namd to calculate energies?
Unlikely, but perhaps they are beyond the cutoff range you specified.
Otherwise, make sure you are reading in the pairlist file correctly
(check the name in your config file).

Eric H. Lee
Medical Scholars Program
Theoretical and Computational Biophysics Group, UIUC

On Jun 21, 2009, at 4:01 PM, Navendu bhatnagar wrote:

> Hello,
> I am trying to calculate pair interaction energies between a protein
> and membrane (system not solvated, gas phase) by analyzing their
> trajectory .dcd files.
> I have set the .conf file as described in the user manual and have
> assigned the appropriate flags in the pair interaction file.
> When I execute the command, in my .log file, I get the forces for
> each time step but my energy values are all zero. In my normal
> simulation I do get energy output.
> Am I missing something here ?
> Thanks,
> Navendu

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