[gmx-users] Dimensionless units question

[Amit Choubey]

On Fri, Jul 29, 2011 at 12:14 PM, Alex Marshall <amarsh59 at uwo.ca> wrote:

> 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.


Why not use 0 for LJ parameters? You will have to figure out the units of
energy and force in the reference otherwise you cannot make the comparison.


>
>
> 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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