[lammps-users] Error about using TIP4P

Dear LAMMPS users,

I am first-time using lj/cut/coul/long/tip4p potential for a 3D periodic water system. Now I am just checking with the pure water molecules, nothing else in the simulation. I am confused why I always got the error “TIP4P hydrogen is missing” or " Out of range atoms - cannot compute PPPM". I checked with my input. There is no overlap atoms and the “timestep” is pretty small, 0.1 fs. Also, the “neighbor” is used with “6.0 bin” and “neigh_modify” is “delay 2 every 1 check yes”.

Does anybody know what else I should to check to find out the problem?

Most appreciate for your help.

Sincerely
Yajie

2009/3/23 Yajie Lei <yajielei@…1044…>

Dear LAMMPS users,

I am first-time using lj/cut/coul/long/tip4p potential for a 3D periodic water system. Now I am just checking with the pure water molecules, nothing else in the simulation. I am confused why I always got the error “TIP4P hydrogen is missing” or " Out of range atoms - cannot compute PPPM". I checked with my input. There is no overlap atoms and the “timestep” is pretty small, 0.1 fs. Also, the “neighbor” is used with “6.0 bin” and “neigh_modify” is “delay 2 every 1 check yes”.

Does anybody know what else I should to check to find out the problem?

Dear Yajie:

Do you get the “TIP4P hydrogen is missing” error on the first time step? If so, this may be a sign that your connectivity for the water molecules is incorrect. The atoms must be listed in consecutive order, with the oxygen first, followed immediately by the two connected H atoms.

–AEI

Dear Ahmed,

Thanks for your reply.

I checked with the input data. It’s fine. The connectivity has no problem. Actually, the error arose after some time steps run, not the first step.

Now I have a question about the connectivity. If the connected hydrogen run over the simulation boundary, can the associated oxygen still identify it with the periodic boundary condition? I am not sure whether my problem was caused by this.

Sincerely
Yajie

If the atoms are in correct order in the input data file
and become lost after some number of timesteps, it's
b/c your system is doing bad dynamics and atoms are
being moved far out of the box. You need to figure
out why that is happening. Viz should help as well
as printing out lots of thermodynamic info to see if
the system is stable.

Steve