Dear all,
I want to use SPC model in my simulation. I found the following instruction on parameterization for water model. But I have a confusion of this.
In SPC model, water molecules are rigid, but the vibration of bonds and angles have been implemented in LAMMPS. So should I still use the parameters of flexible SPC model and then, use the fix shake to rigid the water?
The SPC water model specifies a 3-site rigid water molecule with charges and Lennard-Jones parameters assigned to each of the 3 atoms. In LAMMPS the fix shake command can be used to hold the two O-H bonds and the H-O-H angle rigid. A bond style of harmonic and an angle style of harmonic or charmm should also be used.
best wishes,
Xiaoyu
Dear all,
I want to use SPC model in my simulation. I found the following instruction
on parameterization for water model. But I have a confusion of this.
In SPC model, water molecules are rigid, but the vibration of bonds and
angles have been implemented in LAMMPS. So should I still use the parameters
of flexible SPC model and then, use the fix shake to rigid the water?
SPC as such is a rigid model. however, there are many variants of it
(e.g. SPC/E) and that includes a flexible SPC model as well.
if you want *the* SPC mode, you have to make the bonds rigid, as that
is what the model requires. a flexible models usually have a different
parameterizations, as the flexibility of bonds and angles also results
in some form of polarizability and that needs to be accounted for.
The SPC water model specifies a 3-site rigid water molecule with charges and
Lennard-Jones parameters assigned to each of the 3 atoms. In LAMMPS the fix
shake command can be used to hold the two O-H bonds and the H-O-H angle
rigid. A bond style of harmonic and an angle style of harmonic or charmm
should also be used.
the bond and angle styles and parameters are needed for two purposes.
fix shake uses those to extract the equilibrium values for bond length
and angle from it when formulating the constraints, and shake doesn't
work with minimization, so you need some force constants for bonds and
angles to "hold the molecules together", even though that won't keep
the molecules rigid (but after the first MD step, that should be
corrected for).
axel.
Then how to set the strength for harmonic bond and angle style? Because we can simply take the length and angle part simply from SPC or SPC/E. But I have no idea of set the strength parameters. Or I can borrow the strength term from AMBER of CHARMM.
Then how to set the strength for harmonic bond and angle style? Because we can simply take the length and angle part simply from SPC or SPC/E. But I have no idea of set the strength parameters. Or I can borrow the strength term from AMBER of CHARMM.
something in that neighborhood. i tend to set them 1 or 2 orders of
magnitude larger, so that during minimization the structure is not
deformed too much. if you don't use minimization, you can set it to
anything. it will be completely ignored during MD, when fix shake is
enabled.
axel.