From: Monika Kumari (Monika.Kumari_at_chemistry.iitd.ac.in)
Date: Mon Oct 03 2022 - 00:08:59 CDT
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 <petefred_at_umich.edu> 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 <
> Monika.Kumari_at_chemistry.iitd.ac.in> 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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