<DIV> </DIV><DIV> </DIV><SPAN>On 03/04/12, <B class=name>Andrew DeYoung </B><adeyoung@andrew.cmu.edu> wrote:</SPAN>
<BLOCKQUOTE style="BORDER-LEFT: #00f 1px solid; PADDING-LEFT: 13px; MARGIN-LEFT: 0px" class=iwcQuote cite=mid:DDB5DA0FF8A4464DBE7656D15B629705@DELLXPS410 type="cite">Hi,<br /><br />Is it possible to compute the total electrostatic energy of an atom over<br />time? By "total," I mean including all of the terms (short range Coulomb,<br />1-4 Coulomb, and Ewald), not just the short range Coulomb and 1-4 Coulomb.<br /><br />This question is somewhat related to a question I asked last week (<br /><a href="http://lists.gromacs.org/pipermail/gmx-users/2012-March/069745.html" target=l >http://lists.gromacs.org/pipermail/gmx-users/2012-March/069745.html</A> ), and<br />to which I received a great answer. But my specific question now is: is it<br />possible to calculate the Ewald term due to a particular atom? Or is it<br />impossible to decouple the Ewald calculation among individual atoms or or<br />sets of pairs of atoms? <br /><br />For example, I would like to determine the electrostatic energy between atom<br />455 and the "rest" of the system (i.e., all other atoms in the system). To<br />try this, I added an entry "a" to my .ndx file:<br /><br />[ a ]<br />455<br /><br />I then added a directive to my .mdp file:<br /><br />energygrps = a<br /><br />I then run grompp and mdrun, passing my .ndx file to grompp. (Note: in my<br />.mdp file, I specify that energies should be saved every timestep: nstenergy<br />= 1.) Then I run g_energy on the .edr file that resulted from mdrun. I am<br />given the following energy terms to extract: <br /><br />---<br /> 1 Bond 2 Angle 3 Ryckaert-Bell. 4 LJ-14<br /><br /> 5 Coulomb-14 6 LJ-(SR) 7 Coulomb-(SR) 8<br />Coul.-recip. <br /> 9 Potential 10 Kinetic-En. 11 Total-Energy 12<br />Conserved-En. <br /> 13 Temperature 14 Pressure 15 Constr.-rmsd 16 Vir-XX<br /><br /> 17 Vir-XY 18 Vir-XZ 19 Vir-YX 20 Vir-YY<br /><br /> 21 Vir-YZ 22 Vir-ZX 23 Vir-ZY 24 Vir-ZZ<br /><br /> 25 Pres-XX 26 Pres-XY 27 Pres-XZ 28 Pres-YX<br /><br /> 29 Pres-YY 30 Pres-YZ 31 Pres-ZX 32 Pres-ZY<br /><br /> 33 Pres-ZZ 34 #Surf*SurfTen 35 Mu-X 36 Mu-Y<br /><br /> 37 Mu-Z 38 Coul-SR:a-a 39 LJ-SR:a-a 40 Coul-14:a-a<br /><br /> 41 LJ-14:a-a 42 Coul-SR:a-rest 43 LJ-SR:a-rest 44<br />Coul-14:a-rest<br /> 45 LJ-14:a-rest 46 Coul-SR:rest-rest<br /><br /> 47 LJ-SR:rest-rest 48 Coul-14:rest-rest<br /><br /> 49 LJ-14:rest-rest 50 T-System<br />---<br /><br />Choices 42 and 44 are two parts of what I would like: short range Coulomb<br />and 1-4 Coulomb energy terms for a-rest. But is it possible to somehow also<br />calculate the Ewald term for a-rest?</BLOCKQUOTE>
<DIV> </DIV><DIV>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.</DIV><DIV> </DIV><DIV>Mark </DIV>