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.) 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 -- 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
