I want to use only lj/cut potential for a 38-atom molecule (excluding bonds, angles…), to start with. I am defining pair style as lj/cut with a cutoff distance and pair coefficients and using an initial gaussian velocity distribution. However in my output data, there is drastical increase in temperature at the first steps, reaching to 7 digits from 300K. Also the pair energy is very big.
I tried to define atom sytle as atomic, since I don’t include any angles or dihedrals…But it gives me the error “Incorrect atom format in data file” eventough the same data file works for atom style molecular (which is more general than what I want for the time being). I also tried to change box size and cut off distance, did not help.
With the same parameters and same molecule, including bonding information seems to work fine. From the dump file, I tried to visualize the structure and the motion, it seemed like atoms are flying away, I don’t even see the 38 atoms, just a few, I do not observe bond stretching, for instance. However I used some other tool to construct the structure at every specified timestep and made a movie which was all okey, it is just so much time consuming.
Finally my question is what can I do to fix my lj/cut potential? Also what should I be doing wrong when using xmovie tool for lj/cut + bond interaction system? I know it is wide end question, any help will be appreciated.