LAMPPS Simulation with water

Please post the question to the mailing list, not to me directly.

Cannot compute pppm is a well discussed topic on the list, please search the archive.

You have bad dynamics. First to make sure is that you can run your system without the wall. Then add the wall and visualize the system. There must be something you are missing. You can also use the displace_atoms command to move your water molecules.


Thank you for the suggestions.
It seems I have a bad dynamics due to bad initial condition because I get ‘nan’ for the pressure at timestep 0 for the simulation with water only.
This confuse me because I have used packmol with tolerance distance 3.8 (which is 0.6 more than LJ cutoff value for water) to generate the molecules position.
The energy relaxation using minimize cannot be used due to the fix shake for water.
Is there any way to fix this problem? Does lattice combined with create atoms can be used for good initial condition or is there any other good method?

Thank you,

Yes , your system has bad dynamics and you got to fix this step by step. First make sure you water runs or minimizes without anything. Then add fix shake, then add the wall.