> 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 [email protected] 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
