please always keep the mailing list in cc. thanks.
Thanks for the response.. yes but if i don't put fix shake ,when i am
trying to simulate the code, i see from a xyz file that from for
example a CO2 molecule, C,O,O atoms go very far from each other,like
there is no bond. what should i do? Does anyone can give me a simple
that will depend on whether your data file and your
bond parameters are suitable this is impossible to
tell. have you checked that you are using the correct
units and that - in case you had to convert units -
you were using the correct conversion. the easiest
way to test it, is to set up a system for just one
molecule and cross-check the results that LAMMPS prints
out with a pencil and paper calculation.
example for how can i model a simple molecule?i mean if i omit the fix
shake line everything else is ok? i don't think so because my output
is always the same.nothing change in the energy outputs.
a simulation program follows the GIGO principle. it will do what
you ask it to do. however it cannot read your mind (neither can i),
so *you* have to confirm step by step that whatever you do and
use is correct. thus you should strip down your input to the minimum
and then grow it until you notice the failure.
there are plenty of examples shipped with lammps. in your case,
perhaps the micelle example might be helpful.