[gmx-users] Computing the total electrostatic energy (short range, 1-4, and Ewald) of an atom

Andrew DeYoung adeyoung at andrew.cmu.edu
Tue Apr 3 04:05:51 CEST 2012


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 ]

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
  9  Potential       10  Kinetic-En.     11  Total-Energy    12
 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
 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?

Thank you kindly! 

Andrew DeYoung
Carnegie Mellon University 

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