[gmx-users] Shift functions

[Elisabeth]

On 10 February 2012 09:41, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:

>  On 11/02/2012 1:19 AM, Elisabeth wrote:
>
>
>   Hello all,
>>
>> Does the shift function use group based truncation?
>>
>>
>>  See the discussion of charge groups in manual section 3.4.2.
>>
>
> Thanks Mark.
>
> -1- First of all if I am right  charge groups in gromacs language in
> identical to "group based truncations"?
>
>
> Using charge groups as the indivisible entity upon which neighbour list
> construction is based is using "group based truncations". The usual
> alternative is using atoms as the, well, *atomic* unit. The former can be
> equivalent to the latter if there's one atom per charge group.
>
>
>
>
>  Manual 342: "This reduces the cut-off effects from the charge-charge
> level to the dipole-dipole level, which decay much faster"
>
> 2- I am not able to realize why we go from charge-charge the dipole-dipole
> changes?
>
>
> Charge groups are constructed to have neutral charge (or integer charge
> where necessary). To first order, the difference between any such group
> being in the neighbour list of another such group or not (according to the
> cut-off radius) is equivalent to a point dipole being in the cut-off sphere
> or not. Charge groups with arbitrary charge (or partially-charged atoms,
> when using atom-based truncation) do not have this quality, and the
> distance at which a charge-charge interaction is significant is much larger
> than that of a dipole-dipole.
>
>
>
>
>
>    In the manual I see: by using shifted forces there is no need for
>> charge groups (=group based?!) in the neighbor list?
>>
>> Can anyone shed some light on calculation of shifted forces?
>>
>>
>>  What's not clear from the above and 4.1.5?
>>
>
> 3- I understand that use of shift makes the potentials have continuous
> derivatives at cutoffs but that how this makes use of charge groups
> unnecessary, I dont see!
>
>
> Remember that the neighbour list is constructed to permit the computation
> of a finite number of interactions with the central atom/group. You want to
> stop computing them when they're close enough to zero that you don't care.
> If they actually go to zero, then you don't care. If they decay as 1/r
> (charge-charge) then at typical r_c values you should care. If they decay
> as 1/r^2 (dipole-dipole, IIRC) then at typical r_c values things are OK.
>
> If the value of the force is non-zero at the cut-off, then there is an
> interaction at that distance and not one just past that distance. This
> generates artefacts that are serious for non-zero charges at the kinds of
> cut-off distances for which force fields are parametrized, but much less
> serious if computed over neutral charge groups.
>
> If the value of the force is zero at the cut-off (i.e. shift potential),
> then no atom or charge group has any interaction with the central
> group/atom at that distance,
>



> so you don't need to care about whether the truncation is based on atoms
> or groups. You do have to care about the effect of the modified Coulomb
> potential, however.
>
> Hello Mark,
>

I read over your answer several times. I am still unclear about " modified
Coulomb potential". In the manual modified Coulomb potential refers to
shift/switch functions, as I realized. so when the force is zero at r_c and
it doesnt matter whether truncation is based on atoms or groups, why effect
of modified coulomb potential is important?

>
>
>
>
>
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