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.
Best ragards,
Burcu E.
Hi Burcu. Here are some thoughts and suggestions that
I hope you�ll find useful.
Huge temperatures and energies are typically
indicative of a bad initial configuration and/or force
field setup. My guess for the case you�ve described is
that the atoms in your molecule are bonded and hence
close together, and then you removed all of the bond
and angle terms from the force field, so LAMMPS did
not exclude LJ interactions between those neighboring
atoms that used to be bonded together, which caused
huge repulsions and a spike in T and energy.
Switching to atom style atomic won�t help since the
atoms are too close together (if my guess as to the
problem here is correct). But the reason for the error
message is that the data file format requirements are
different for the different atom styles. So you�d have
to change the format of your data file if you really
wanted to do atom style atomic. See the �atoms�
section here:
http://www.cs.sandia.gov/~sjplimp/lammps/doc/read_data.html
Another possible problem is that the units you specify
in your input file do not agree with the units in your
data file. Are you using LJ units in both places, or
real units in both places?
I don�t know a lot about using xmovie, but there are a
wide range of visualization tools available that you
might try. I personally use VMD a lot:
http://www.ks.uiuc.edu/Research/vmd/
You can tell LAMMPS to dump coordinates in the *.xyz
format:
http://www.cs.sandia.gov/~sjplimp/lammps/doc/dump_modify.html
and VMD will read in files produced in this way. (Or
you can convert LAMMPS output to pdb file(s) and use
those in VMD.)
If you need assistance beyond this, it would be
helpful if you posted your input script and data file
(if they are small --- sounds like they are). Or just
e-mail them to me and I�ll take a look at them.
Good luck!
Paul