CHARMM TIP3P

For regin TIP3P-CHARMM water model, I wrote the input file like this:

units real
atom_style full
boundary p p p

read_data 00.data.lammps

group water type 1 2

bond_style harmonic
bond_coeff 1 450 0.9572
angle_style harmonic
angle_coeff 1 55 104.52
pair_style lj/cut/coul/long 12.0
pair_coeff 1 1 0.1521 3.15061 12.000
pair_coeff 1 2 0.0836 1.77530 12.000
pair_coeff 2 2 0.0460 0.40000 12.000

kspace_style pppm 0.0001
special_bonds lj/coul 0.0 0.0 0
neighbor 2.0 bin
neigh_modify delay 0 one 2000 check yes

timestep 1.0
thermo_style custom step temp etotal

velocity water create 300.0

min_style cg
min_modify dmax 1.0
minimize 0.01 0.001 1000 1000000
thermo_style custom step temp etotal press

thermo_modify flush yes line one

thermo 100

fix regidwater water shake 0.0001 10 10 b 1 a 1

fix 2 water npt temp 300.0 300.0 100.0 z 1.00 1.00 1000.0
run 500000
unfix 2

But I think I should not use both 'fix SHAKE ’ and harmonic bond/angle at the same time.

Thanks,

Hangyan

2011-09-23

2011/9/23 physics.hangyan.chen <[email protected]...>:

For regin TIP3P-CHARMM water model, I wrote the input file like this:

But I think I should not use both 'fix SHAKE ' and harmonic bond/angle at
the same time.

you _have_ to. how do you think fix shake would otherwise know what
your desire bond length or angle would be?

since you are also running minimizations, you should increase the
force constants on both (at least during minimization, i use a factor
of 100) so that the water molecules don't stretch and bend too much.

in combination with shake, the force constants have no meaning.

axel.