[gmx-users] Computing the total electrostatic energy (short range, 1-4, and Ewald) of an atom
Mark Abraham
mark.abraham at anu.edu.au
Tue Apr 3 07:16:22 CEST 2012
On 03/04/12, Andrew DeYoung <adeyoung at andrew.cmu.edu> wrote:
> Hi,
>
> Is it possible to compute the total electrostatic energy of an atom over
> time? By "total," I mean including all of the terms (short range Coulomb,
> 1-4 Coulomb, and Ewald), not just the short range Coulomb and 1-4 Coulomb.
>
> This question is somewhat related to a question I asked last week (
> http://lists.gromacs.org/pipermail/gmx-users/2012-March/069745.html ), and
> to which I received a great answer. But my specific question now is: is it
> possible to calculate the Ewald term due to a particular atom? Or is it
> impossible to decouple the Ewald calculation among individual atoms or or
> sets of pairs of atoms?
>
> For example, I would like to determine the electrostatic energy between atom
> 455 and the "rest" of the system (i.e., all other atoms in the system). To
> try this, I added an entry "a" to my .ndx file:
>
> [ a ]
> 455
>
> I then added a directive to my .mdp file:
>
> energygrps = a
>
> I then run grompp and mdrun, passing my .ndx file to grompp. (Note: in my
> .mdp file, I specify that energies should be saved every timestep: nstenergy
> = 1.) Then I run g_energy on the .edr file that resulted from mdrun. I am
> given the following energy terms to extract:
>
> ---
> 1 Bond 2 Angle 3 Ryckaert-Bell. 4 LJ-14
>
> 5 Coulomb-14 6 LJ-(SR) 7 Coulomb-(SR) 8
> Coul.-recip.
> 9 Potential 10 Kinetic-En. 11 Total-Energy 12
> Conserved-En.
> 13 Temperature 14 Pressure 15 Constr.-rmsd 16 Vir-XX
>
> 17 Vir-XY 18 Vir-XZ 19 Vir-YX 20 Vir-YY
>
> 21 Vir-YZ 22 Vir-ZX 23 Vir-ZY 24 Vir-ZZ
>
> 25 Pres-XX 26 Pres-XY 27 Pres-XZ 28 Pres-YX
>
> 29 Pres-YY 30 Pres-YZ 31 Pres-ZX 32 Pres-ZY
>
> 33 Pres-ZZ 34 #Surf*SurfTen 35 Mu-X 36 Mu-Y
>
> 37 Mu-Z 38 Coul-SR:a-a 39 LJ-SR:a-a 40 Coul-14:a-a
>
> 41 LJ-14:a-a 42 Coul-SR:a-rest 43 LJ-SR:a-rest 44
> Coul-14:a-rest
> 45 LJ-14:a-rest 46 Coul-SR:rest-rest
>
> 47 LJ-SR:rest-rest 48 Coul-14:rest-rest
>
> 49 LJ-14:rest-rest 50 T-System
> ---
>
> Choices 42 and 44 are two parts of what I would like: short range Coulomb
> and 1-4 Coulomb energy terms for a-rest. But is it possible to somehow also
> calculate the Ewald term for a-rest?
Not easily, and the value of it would be debatable even if you could compute it. Someone did post a several-step method a few years ago using mdrun -rerun and perhaps tpbconv -zeroq that achieved something like the decomposition of the reciprocal-space term you seem to be after.
Mark
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