Hello All,
I am trying to restrain bonds involving hydrogen atoms using the following fix
fix 1 all shake 1e-6 500 0 m 1.0 #SHAKE is applied on Hydrogen atoms
and I keep getting the error, Shake clusters are connected.
The “common errors” page on lammps.sandia.gov describes it as: A single cluster specified by the fix shake command must have a single central atom with up to 3 other atoms bonded to it.
I then tried to run NVT to check if the bonds information is correct and the simulation ran just fine. What should/shouldn’t I do to restrain the hydrogen atoms ?
Thank for your time,
Pavan
The input script is:
units real
neigh_modify delay 2 every 1
atom_style full
bond_style harmonic
angle_style harmonic
dihedral_style harmonic
pair_style lj/charmm/coul/long 8 10
pair_modify mix arithmetic
kspace_style pppm 0.00008
read_data data.in
special_bonds amber
thermo 1000
thermo_style multi
timestep 1
fix 1 all shake 1e-6 500 0 m 1.0 #SHAKE is applied on Hydrogen atoms
fix 2 all npt 312.0 312.0 100.0 xyz 1.0 1.0 1000.0 #Performing a NPT simulation with an isotropic pressure of 1atm.
velocity all create 0.0 12345678 dist uniform
restart 1000 proj.restart1 proj.restart2
dump 2 all atom 1000 proj_nvt.dump
dump_modify 2 image yes scale yes
run 300000