From: Monika Kumari (Monika.Kumari_at_chemistry.iitd.ac.in)
Date: Mon Oct 10 2022 - 00:57:02 CDT
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 <
Monika.Kumari_at_chemistry.iitd.ac.in> 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 <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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