Dear Users and Developers,
I'm trying to study such a solid system that there are bonds, angles. Also atoms are charged so there are coulombic interactions but no other pairwise interactions. in the input file, for the coulombic interaction part, I have:
kspace_style ewald 1e-6
pair_style coul/long 10.0
pair_coeff * *
special_bonds coul 1 1 1
questions:
1. no matter what special_bonds coefficients are set, 1-3, 1-4 bond contributions to energy and force will always be counted, is that correct?
2. If I want to always count the coulombic interaction among atoms no matter they are bonded or not, I should set special_bonds coul 1 1 1, is that correct?
3. If I set special_bonds coul 0 0 0, then for those 1-2, 1-3, 1-4 bonded atoms, coulombic interaction will not be counted, is that correct?
Thanks a lot for your help!
Bo
Dear Users and Developers,
I'm trying to study such a solid system that there are bonds, angles.
Also atoms are charged so there are coulombic interactions but no other
pairwise interactions. in the input file, for the coulombic interaction
part, I have:
kspace_style ewald 1e-6
pair_style coul/long 10.0
pair_coeff * *
special_bonds coul 1 1 1
questions:
1. no matter what special_bonds coefficients are set, 1-3, 1-4 bond
contributions to energy and force will always be counted, is that correct?
yes. special_bonds holds scaling factors for non-bonded.
the direct bonded contributions are controlled over their parameters.
2. If I want to always count the coulombic interaction among atoms no
matter they are bonded or not, I should set special_bonds coul 1 1 1, is
that correct?
yes.
3. If I set special_bonds coul 0 0 0, then for those 1-2, 1-3, 1-4
bonded atoms, coulombic interaction will not be counted, is that correct?
yes.
Thanks a lot for your help!
you are welcome,
axel.
Axel,
Thanks for your reply! One more question:
if my input file looks like:
Axel,
Thanks for your reply! One more question:
if my input file looks like:
read_data data
bond_style morse
bond_coeff 1 0.974 1.2848 3.10 #only between atom type1 and type2
kspace_style ewald 1e-6
pair_style coul/long 11.0
pair_coeff * *
special_bonds coul 1 1 1
velocity all create 300.0 873586443 temp 1
......
if I have a toy system with four charged atoms : index(atom type)
1(1)--2(2)--3(1)--4(2)
then from topology, it will be found that
1-2 bond:
1-2, 2-3, 3-4
1-3 bond:
1-3, 2-4
1-4 bond:
1-4
is it true that 1-3, 2-4 bond energy/force will be zero since (1)-(1),
(2)-(2) bonds are not defined?
is it true that 1-4 bond energy/force will be computed from the defined
(1)-(2) bond parameter and their distance?
if I set special_bonds 0 0 0, is it true that coulombic interaction for only
1-3, 2-4 will be counted?
is there a way to turn off the 1-3, 1-4 bond contribution?
i don't fully understand what your system is and what you
are asking. but you can surely answer all your questions
by selectively turning interactions on and off and defining
and undefining bonds.
Another observation I made is from a simpler toy system with 2 atoms
1(1)-2(2) sitting in a huge box,
by setting sepcial_bonds 0 0 0, no coulombic interaction should be counted,
however, from thermo_style output of "ecoul", I still see a non-zero value,
why is that?
i don't know. you may have set the wrong scaling factors
you have to use special_bonds coul or special_bonds lj/coul.