2012/1/13 陈航燕 <[email protected]...>:
Thanks very much,Steve.
I tried 'fix co2 rigid/nvt molecule temp 300.0 300.0 100.0' and got some
1) When I finish the equilibrium for 1 ns. The new calculation can only
start from the restart file. When I tried to have the calculation start from
the data file (which is generated by dump command) after the equilibrium of
1 ns. I always got the error: 'Fix rigid: Bad principal moments'. I use the
fix rigid/nvt for the calculation, the bond and angle for those co2
molecules should not change during the simulation? Why I still have the
error which seems like the angles are not exactly 180 degree?
this is difficult to say without seeing your input.
could be that you are missing the image flags
or are not dumping unwrapped coordinates.
once a molecule straddles the periodic boundary,
you get an unphysical geometry, unless you use
unwrapped coordinates or image flags.
2)I want to simulate the transportation of co2 in carbon nanotube. I have
the same problem as mentioned above. I am not sure if I miss something
the "garbage in, garbage out" principle holds
for any system. if you cannot get the pure system
to work correctly, why should it be different
for a compound system.
3)In the calculation, I found the bond energy and angle energy are not
exactly zero, but very small, say 0.002 kcal/mol. As I think, if I use rigid
model, the bond/angle energy should be exactly zero, right?If I use the fix
no. LAMMPS does what you tell it to do. bond/angle forces and energies
are always computed and added to the total force if you have a bond and/or
angle style defined. the rigid integrator takes the total forces on each atom,
and then separates them into a translational and rotational component,
and then integrates the positions of the atoms accordingly (based on
center of mass and the moments of inertia). if you don't want bond and
angle terms to be computed, you have to turn them off, e.g. by using
the "none" style.
rigid/nvt command for the calculation, do I need to specify the bond and
angle parameters in the input files? For example: Bonds, angles, bond length
and force constant.
no. the rigid integrator only looks for rigid bodies according to the specs;
for molecules, it is the molecule id.