[gmx-users] Dimensionless units question

Alex Marshall amarsh59 at uwo.ca
Fri Jul 29 21:14:32 CEST 2011


I'm trying to calculate the total electrostatic energy of the system, and
the force in the Z direction on the particle placed above the lattice. It's
a purely electrostatic problem, ideally LJ shouldn't come into it at all,
but I don't know how else to convert the resulting energy and force to
dimensionless units, which I must do because I was given reference values in
dimensionless units.

I guess I'm not actually using gmx.ff, I was just using the C6-C12
convention for LJ parameters used in that forcefield's ffnonbonded.itp.

On Fri, Jul 29, 2011 at 3:50 PM, Amit Choubey <kgp.amit at gmail.com> wrote:

> I am not sure what you want to measure. You mentioned that "force and
> energy I calculate are still quite far from the reference values", now are
> you only looking at electrostatic contributions to these or the total
> contributions? If its total contribution then LJ parameters should also be
> correct and for that you should switch to standard gromacs units.
>
> Also why do you need to use gmx.ff, seems to me that you already have the
> parameters (ie the LJ parameters and charges)
>
>
> On Fri, Jul 29, 2011 at 11:30 AM, Alex Marshall <amarsh59 at uwo.ca> wrote:
>
>> Hi Amit,
>>
>> So if I understand you correctly, any LJ interaction I impose on these
>> particles will be quite arbitrary because I'm only concerned with
>> electrostatics, right? How then might I go about comparing the dimensionless
>> reference values given with the values I calculated? I don't think I can
>> simply compare their ratios, as there would still be a unit of length to
>> deal with.
>>
>> Thanks,
>> Alex
>>
>> On Fri, Jul 29, 2011 at 2:24 PM, Amit Choubey <kgp.amit at gmail.com> wrote:
>>
>>> Hi,
>>>
>>> reduced units works for LJ particles only. I am not sure if it works when
>>> you include electrostatics. When you set charge = 1 it is 1electronic
>>> charge. I would suggest not to use the reduced units for LJ in this
>>> scenario.
>>>
>>> Amit
>>>
>>> On Fri, Jul 29, 2011 at 8:05 AM, Alex Marshall <amarsh59 at uwo.ca> wrote:
>>>
>>>> Hi all,
>>>>
>>>> I'm trying to calculate the force on one particle and the total
>>>> electrostatic energy of my system, which consists of a lattice of 25 evenly
>>>> spaced charges in the xy plane and a single charge in the center above to
>>>> preserve charge neutrality. The reference values I have been given are in
>>>> dimensionless units, so I am tasked with either converting my output to
>>>> dimensionless units or having gromacs work in reduced units from the get go.
>>>> I have set the mass of each charge to 1, the magnitude of the charge on each
>>>> particle to 1, and the values of the C6 and C12 parameters in my itp file to
>>>> 4.0, since I'm just using gmx.ff for this (hopefully simple) calculation.
>>>> I've turned off temperature coupling because this is purely a test of the
>>>> handling of electrostatics with 3D Ewald summation plus the correction for
>>>> slab geometry. However, the force and energy I calculate are still quite far
>>>> from the reference values. Have I missed anything if I want my output to be
>>>> in dimensionless units?
>>>>
>>>> Thanks,
>>>> Alex
>>>>
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>>>
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>
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