Including Dummy-Site Coordinates of TIP4P/2005 Water in Data File
From: Sang Beom Kim <sangbk@Princeton.EDU> - 2013-12-30 04:26:07Dear LAMMPS Users,I am currently trying to make a data file which contains proteins and TIP4P/2005 waters. I know there are TIP4P-specific options such as lj/cut/tip4p/long orpppm/tip4p without explicitly specifying the coordinates of dummy site in the date file. However, for a specific reason, I would like to include the coordinates of dummy sites in the data file and just use regular options of lj/cut/coul/long and pppm. And for my purpose, I just need to generate a configuration for an analysis purpose (not planning on running simulation with this configuration).
In order to check if I have generated a correct file, I check energies (short-range LJ, short-range coulomb, long-range coulomb, etc.). I check by comparing with the energies calculated by using GROMACS and in-house code. The only discrepancy I am seeing is with the electrostatic energies when I use the Ewald or PPPM. If I just use cut-off at a certain distance (for electrostatics), the energies match very well, but only when I use Ewald or PPPM there are discrepancies in electrostatic energies (both short and long ranges). I specifically need to use lj/cut/coul/long option with either ewald or pppm, and I was wondering what I am setting wrong. The proteins are no problem. Any suggestions on this issue would be greatly appreciated. The following is the input I am using: ------------------------------------------------------------------------------------------------------------- special_bonds amber bond_style harmonic angle_style harmonic dihedral_style harmonic improper_style none pair_style lj/cut/coul/long 10.00000 10.000000 pair_modify mix arithmetic kspace_style ewald 1.0e-4 dielectric 1.000000 # neighbor list update neighbor 0.000000 bin neigh_modify every 1 delay 0 check no once no # water (20 - oxygen, 21 - hydrogen, 22 - dummy site) group water type 20 21 22 neigh_modify exclude molecule water fix 1 water shake 0.0001 20 0 b 26 a 38 -------------------------------------------------------------------------------------------------------------- Thank you, Sang Beom Kim Chemical and Biological Engineering Princeton University
Re: [lammps-users] Including Dummy-Site Coordinates of TIP4P/2005 Water in Data File
From: Axel Kohlmeyer <akohlmey@gm...> - 2013-12-30 05:40:11
make a less complex input, e.g. one that you can compute by hand and
then you should *much* more carefully investigate how to synchronize
the settings for long-range electrostatics to make those codes match
(close enough). there may also be implementation specific differences
(gromacs applies its cutoff to charge groups, not individual atoms)
also PPPM is different from (S)PME and different codes use different
estimators for kspace parameters. 1.-e-4 is very sloppy. you are
likely to only get agreement, if you choose a very narrow kspace
convergence in all codes.