Dear Lammps Users,
I am new to this program and this system so I beg you to forgive any primitive errors I might be making. I am currently working on modelling SPC/e water with a molecule of CaCl2 in it. Without the CaCl2 Molecule, I was able to run the simulation successfully; however, upon adding the molecule, and removing the appropriate water molecule to make space, my simulation was crashing because the PPPM algorithm was unable to compute values because the Hydrogen atoms were moving too close to each other (atoms out of range). I am attaching my input script, the control file, and the output (xyz, dcd, and save files). Could you please advise me as to how to solve this issue? Note that this only occurs when the shake fix is used. Thank you very much for taking time to help me.
Sincerely,
Pridhvi M.
control01 (1.27 KB)
log.lammps (3.13 KB)
Test.dcd (176 KB)
test.lj (244 KB)
test.save (462 KB)
Test.xyz (61.6 KB)
Dear Lammps Users,
I am new to this program and this system so I beg you to forgive any
primitive errors I might be making. I am currently working on modelling
SPC/e water with a molecule of CaCl2 in it. Without the CaCl2 Molecule, I
was able to run the simulation successfully; however, upon adding the
it still is unlikely to be correct. your data file does not conform to
the requirements. e.g. for angles the center atom has to be given as
the second atom, but in your data file you have: bonds 2-1 and 3-1 but
angle 1-2-3. however, in this case the angle must be defined as 2-1-3
molecule, and removing the appropriate water molecule to make space, my
simulation was crashing because the PPPM algorithm was unable to compute
values because the Hydrogen atoms were moving too close to each other (atoms
out of range). I am attaching my input script, the control file, and the
out of range doesn't mean too close, it means that they moved too
fast. that is usually a consequence of bad potential parameters, bad
simulation settings or an initial geometry with very high potential
energy, or a combination of those.
output (xyz, dcd, and save files). Could you please advise me as to how to
solve this issue? Note that this only occurs when the shake fix is used.
you have a combination of problems. the "folding" of atoms is a
consequence of the incorrect angle assignments. the out of range atoms
is due to a different set of possible reasons listed above. i suggest
you first set up *and validate* a simulation with pure water. there is
plenty of reference data on SPC/E in the literature...
axel.