On 4/04/2012 12:11 AM, Andrew DeYoung wrote:
Greetings,
Thank you so much, Mark!
Do you know if it is possible to extract just the real-space part (not the
reciprocal space part) of the Ewald summation? (By "Ewald summation," I
mean either the standard Ewald summation or PME.)
That's what Coul-SR is.
Mark
Thank you very much!
Andrew DeYoung
Carnegie Mellon University
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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