Dear all,
I used the typical LJ parameters and the DREIDING force field to water system.
///////////////////////////////////////////////
pair_style hybrid/overlay hbond/dreiding/lj 4 7.5 160 lj/cut 8.0
bond_style harmonic
angle_style harmonic
pair_coeff 1 1 lj/cut 0.004150 3.03 # O-O LJ
pair_coeff 1 2 hbond/dreiding/lj 2 i 0.075889 2.75 # O-H hbond
pair_coeff 1 2 lj/cut 0.000134 2.94 # O-H LJ
pair_coeff 2 2 lj/cut 0.000004 2.85 # H-H LJ
bond_coeff 1 30.36 0.98 # O-H bond
angle_coeff 1 4.63 104.51 # H-O-H angle
mass 1 16.0 # O
mass 2 1.0 # H
///////////////////////////////////////////////
These settings can work, but the features of hbond do not appear. I have three problems:
1. I think that the force contributed by LJ and hbond are co-existence. Is the "hybrid/overlay" command right?
2. Hbond is the interaction between O and H. Is the setting of "pair_coeff 1 2 hbond/dreiding/lj" correct? (I,J->1,2)
3. The manual says: "If the donor flag is i, then the atom of type I in the pair_coeff command is treated as the donor, and J is the acceptor."
But the figure in manual illustrated that both the donor and acceptor are oxygen atom. So, I am confused about this.
Thanks!
T.H. Liu
Perhaps Tod can answer these Qs.
Steve
Te-Han:
I used the typical LJ parameters and the DREIDING force field to water
system.
///////////////////////////////////////////////
pair_style hybrid/overlay hbond/dreiding/lj 4 7.5 160 lj/cut
8.0 bond_style harmonic angle_style harmonic
pair_coeff 1 1 lj/cut 0.004150 3.03 # O-O LJ
pair_coeff 1 2 hbond/dreiding/lj 2 i 0.075889 2.75 # O-H
hbond pair_coeff 1 2 lj/cut 0.000134 2.94 #
O-H LJ pair_coeff 2 2 lj/cut 0.000004 2.85 #
H-H LJ bond_coeff 1 30.36 0.98 #
O-H bond angle_coeff 1 4.63 104.51
# H-O-H angle mass 1 16.0
# O mass 2 1.0 # H
///////////////////////////////////////////////
These settings can work, but the features of hbond do not appear. I
have three problems:
1. I think that the force contributed by LJ and hbond are
co-existence. Is the "hybrid/overlay" command right?
Correct
2. Hbond is the interaction between O and H. Is the setting of
"pair_coeff 1 2 hbond/dreiding/lj" correct? (I,J->1,2)
No. Should be pair_coeff 1 1 hbond/dreiding/lj 2 ...
The pair coeff should be between the acceptor and donor atom types as
specified in the manual
3. The manual says: "If the donor flag is i, then the atom of type I
in the pair_coeff command is treated as the donor, and J is the
acceptor."
But the figure in manual illustrated that both the donor and
acceptor are oxygen atom. So, I am confused about this.
Since both donor and acceptor are the same atom type, either i or j would
work
BTW: your angle cutoff seem rather restrictive. This means that only
interactions between 180 +/- 20 degrees will be counted.
The safe value would be 90 so that all interactions (180 +/- 90) would be
counted.
Also, note that the hbond syntax has changed in the latest version of LAMMPS
such that the distances are now splined smoothly to zero between an inner
and outer cutoff. This leads to more stable dynamics.
Tod
Dear Tod,
Thanks for your kind advice. I have reset the parameters by your suggestions, and the expected features of hbond appear!
Thanks!
T.H Liu
///////////////////////////////////////////////////////////////////////
pair_style hybrid/overlay hbond/dreiding/lj 4 7.5 7.5 75.0 lj/cut 8.0
bond_style harmonic
angle_style harmonic
pair_coeff 1 1 hbond/dreiding/lj 2 i 0.075889 2.75
pair_coeff 1 1 lj/cut 0.004150 3.03
pair_coeff 1 2 lj/cut 0.000134 2.94
pair_coeff 2 2 lj/cut 0.000004 2.85
bond_coeff 1 30.36 0.98
angle_coeff 1 4.63 104.51
mass 1 16.0
mass 2 1.0
///////////////////////////////////////////////////////////////////////
引述 Tod A Pascal <[email protected]...>: