you are right. it was not intentional.
this is the data file attached. it is consisted of only two graphene sheets interacting with each other.
and this is the header of data file:
LAMMPS data file. CGCMM style. atom_style full generated by VMD/TopoTools v1.2 on Mon Dec 31 12:46:34 IRST 2012
360 atoms
502 bonds
932 angles
1742 dihedrals
1 atom types
1 bond types
1 angle types
1 dihedral types
-130.03459 290.966541 xlo xhi
-120.6557 310.977876 ylo yhi
-470.115617 520.884383 zlo zhi
Pair Coeffs
1 0.35 3.74
Bond Coeffs
1 322.55 1.4
Angle Coeffs
1 53.35 120.0
Dihedral Coeffs
1 3.15 1 3
Masses
1 12.010700 # CA
thank you
…
graph.data (78.3 KB)
you are right. it was not intentional.
this is the data file attached. it is consisted of only two graphene sheets
interacting with each other.
ok. so looking at what you are doing
i can only conclude that it doesn't
make any sense. steered MD *cannot*
work for your system and in fact is
great waste of time.
haven't you seen the lines in the
output with WARNING?
you are time integrating all atoms
twice, once using fix rigid, and a
second time with fix nvt. this *will*
lead to completely bogus trajectories.
(as has been discussed on this mailing list
a great many times and is mentioned in the
LAMMPS documentation in multiple locations).
furthermore through using fix rigid
you are removing almost all degrees
of freedom. there is not really a
potential of mean force to be had for
this kind of system. you can just
statically map out the potential energy
and be done. ...and even that can
be done analytically, by just integrating
over the potential in the direction of the
graphene plane and what is left is the
potential that you are looking for.
with a bogus input data,
you get bogus output.
simple as that.
axel.
appreciate your help. I should study more about this.
best regards