i see. i reran the trajectory with reaction field electrostatics and that gave a more negative energy value which was closer to what i was expecting.
i guess the missing reciprocal space contributions explains this discrepancy. is there a way to get the full interaction energy with PME ? thnx for the reply -sandeep On Nov 17, 2007 8:18 PM, Mark Abraham <[EMAIL PROTECTED]> wrote: > > Hi All > > > > I simulated a cubic box of 2180 TIP3P water molecules using gmx 3.3 and > PME > > for 400 ps and extracted the interaction energy of a randomly picked > water > > molecule with rest of the system. > > Simulation was done at 298K and 1bar and usual procedure for generating > a > > water box and equilibration were used. > > > > Average interaction energy reported in the log file was > > Epot (kJ/mol) Coul-SR LJ-SR > > WAT-rest -8.13828e+01 1.21886e+01 > > > > giving a total of -8.13828e+01 + 1.21886e+01 = -69.194 kJ/mol > > > > Comparing with published numbers using other MD programs this should be > in > > the range of -81 +/- 1 kJ/mol i.e. ~11 kJ/mol less. > > > > any clues on origin of this discrepancy ? relevant .top , .mdp files > are > > below. > > The PME algorithm does an approximation to the full periodic Coulomb > summation, but does so with a calculation in direct space, as above, and > another in reciprocal space, where your energy groups are not meaningful. > So you're only getting the direct-space component of the interaction > energy. > > Mark > > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php >
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