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? Thank you kindly! Andrew DeYoung Carnegie Mellon University -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
