Dear lammps users
I have a system consist : DHA molecules, graphen sheet and water.
Input is :
units real
atom_style full
neighbor 1 bin
neigh_modify delay 2 every 1
bond_style harmonic
angle_style charmm
dihedral_style charmm
improper_style harmonic
pair_style lj/charmm/coul/long 8 10
pair_modify mix arithmetic
kspace_style pppm 1e-4
neigh_modify exclude type 12 12
read_data ionized.data
group CA type 12
fix 1 CA setforce 0.0 0.0 0.0
thermo 200
thermo_style custom step temp pe etotal press vol ke enthalpy evdwl epair ebond eangle edihed
minimize 0 0 100000 1000000
special_bonds charmm
dump npt all dcd 5000 ionized-npt.dcd
fix 2 all npt temp 298.0 298.0 100.0 y 1.0 1.0 500
run 2000000
unfix 2
undump npt
fix 3 all nvt temp 298.0 298.0 100.0
fix 4 all shake 1e-6 500 0 m 1.0 a 17
velocity all create 180.0 12345678 rot yes mom yes dist gaussian
velocity CA create 0.0 12345678 rot yes mom yes dist gaussian
timestep 0.5
restart 10 ionized.restart1 ionized.restart2
dump 1 all dcd 5000 ionized.dcd
#dump_modify 1 image yes scale yes
run 5000000
The results after run show the DHA molecules move to side instead center of sheet.
Are the pressure and timestap acceptable for my system?
Do you have any other suggestion ?
Dear lammps users
I have a system consist : DHA molecules, graphen sheet and water.
Input is :
[...]
The results after run show the DHA molecules move to side instead center of
sheet.
Are the pressure and timestap acceptable for my system?
Do you have any other suggestion ?
are you sure that you sent your e-mail to the right address?
it reads as if it was mean to go to [email protected]...
there are a gazillion possible reasons, if a system doesn't behave as
you desire. only some of them have their origin in the choice of
settings in the input file, and even less can be spotted by a casual
look at it. nobody here has a magic crystal ball, so i guess you are
down to doing things the hard way, just like everybody else:
- set up simpler systems that have only one component each and verify
the settings for each of them
- start with a simpler input file and build the complexity of the
input file in stages until you see which part is a main influence on
the undesired behavior
- start thinking whether the behavior if the simulation is actually
physical and your expectation is wrong. build hypotheses in each line
of thought and try to find ways to prove or disprove them until what
you have left is the only logical and meaningful conclusion. in other
words, use the scientific method.
all of these are things that you yourself are in the best position to do.
axel.