Dear lammps users,
I"ve been looking for an initial configuration or just the positions of the 4 atoms used in the TIP4P/2005 model of water. Where the 4th particle is massless but with charge in the middle of the H-O-H angle.
I know that lammps can simulate with the lj/cut/tip4p/cut or …/long potential, but I have several problems finding an initial configuration to simulate.
Does anyone know where I can find a source code or files to generate with something like VMD ?
Thanks
When you are using a “tip4p” pair style, you do not provide the coordinates for the M position. Those will be computed on-the-fly by the pair style and the neighbor list entry for the water oxygen is used for the position of the M site and thus it is saving a lot of time when computing interactions since you have fewer sites to consider for an O(N**2) operation.
for a 3 site water model you can use a TIP3P geometry (which is the same for oxygen and hydrogen as TIP4P) or any other 3-site water since due to using fix shake to constrain the geometry the originally different distances and angles will be reset to the constrained values after a couple of MD steps, i.e. at the beginning of equilibration.
If you want to specify all sites explicitly you must not use a “tip4p” pair style, but rather the regular “coul” pair styles and then you must use fix rigid or fix rigid/small or one of their variants to keep the structure rigid, since you cannot use fix shake or fix rattle.
building the tip4p geometry is rather straightforward if you look up the publication. you can also use a molecule file and the LAMMPS create_atoms command to build an initial system.
there are also bulk water data files in the example folders. you can adjust the size easily by using the replicate command.
it should also be possible to build a water box using one of the pre-processing tools listed on the LAMMPS homepage.
Thanks! That info was really helpful !!