Re: NAMD Energy Plugin giving incorrect energies

From: Peter Freddolino (
Date: Sun Oct 16 2022 - 15:53:21 CDT

Actually after a bit more thought, I think this just has to do with where
one sets the reference point for the electrostatic energy. In an aperiodic
system this is easy -- it is zero at infinite distance. But in a periodic
system there has to be a reference point somewhere that is zero, and it
can't be at infinite separation because that doesn't exist, and when you
have PME on the images and charges can always 'see' each other.

In any case, since dynamics are only affected by the gradient of the
energy, and most other calculations that one might want to do make use of
differences in energy between states, the reference point shouldn't matter
as long as it is consistent.

I didn't run enough tests to figure out exactly what controls where the
zero point occurs in the test system I was playing with, but again, it
doesn't matter for either the dynamics or for thermodynamic calculations
that one might want to do. (out of curiosity, does anyone on this list know
how this behaves if, say, you've just got an interaction between a pair of
ions? How is the reference point determined in the NAMD PME implementation?)


On Mon, Oct 10, 2022 at 1:58 AM Monika Kumari <> wrote:

> Hi Peter,
> It would be very kind of you to have a look at the conf file for any
> suspicious cause for the negative sodium-sodium interaction energies.
> Any suggestions from others are also welcome.
> Thanks in advance.
> Best,
> Monika
> On Mon, 3 Oct 2022 at 10:38, Monika Kumari <
>> wrote:
>> Hi Peter,
>> Thanks for the reply. Pasted below is the used config file. I am using
>> PME and the system is neutral (TOTAL CHARGE = 2.62782e-05 e). I also
>> calculated the interaction energy by turning on and off the debug flag but
>> the output is the same and there was no change in the config file.
>> ##____config file___________
>> structure ionized.psf
>> paraTypeCharmm on
>> parameters toppar/par_all36m_prot.prm
>> parameters toppar/par_all36_na.prm
>> parameters toppar/par_all36_carb.prm
>> parameters toppar/par_all36_lipid.prm
>> parameters toppar/par_all36_cgenff.prm
>> parameters toppar/toppar_water_ions.str
>> numsteps 1
>> exclude scaled1-4
>> outputname sod-sod
>> temperature 0
>> COMmotion yes
>> cutoff 12
>> dielectric 1.0
>> extendedSystem sod-sod.xsc
>> PME on
>> PMEGridSizeX 134
>> PMEGridSizeY 151
>> PMEGridSizeZ 148
>> switchdist 10
>> pairInteraction on
>> pairInteractionGroup1 1
>> pairInteractionFile debug-temp.pdb
>> pairInteractionGroup2 2
>> coordinates debug-temp.pdb
>> set ts 0
>> coorfile open dcd debug-temp.dcd
>> while { ![coorfile read] } {
>> firstTimestep $ts
>> run 0
>> incr ts 1
>> }
>> coorfile close
>> best,
>> Monika
>> On Mon, 3 Oct 2022 at 00:54, Peter Freddolino <> wrote:
>>> That seems... unlikely. Can you please give the precise settings that
>>> you used for namdenergy, ideally including the config files generated by
>>> turning on the debug flag? Are you using PME? Is your system neutral?
>>> Thanks,
>>> Peter
>>> On Tue, Sep 27, 2022 at 11:34 AM Monika Kumari <
>>>> wrote:
>>>> Dear all,
>>>> I am working on a bilayer system in presence of NaCl salt. I calculated
>>>> pair interaction energies of two (random) sodium ions for some timeframes.
>>>> However, the plugin is giving negative interaction energies (~-2.5
>>>> kcal/mol) for most of the frames which I believe is not possible under any
>>>> conditions for two cations. I don't know where I can go wrong.
>>>> Is there anyone who has encountered the same issue? I would be grateful
>>>> for the helpful suggestions.
>>>> Thanks.
>>>> Best,
>>>> Monika
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