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lammps/examples/USER/fep/CH4hyd/fep01/in.fep01.lmp
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in.fep01.lmp
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# created by fftool
print "Methane in TIP4P water"
units real
boundary p p p
atom_style full
bond_style harmonic
angle_style harmonic
special_bonds lj/coul 0.0 0.0 0.5
read_data data.lmp
pair_style hybrid &
lj/cut/coul/long 10.0 10.0 &
lj/cut/tip4p/long/soft 3 4 2 2 0.125 1 0.5 10.0 10.0 10.0
pair_modify tail no
kspace_style pppm/tip4p 1.0e-4
pair_coeff 1 1 lj/cut/coul/long 0.0660 3.5000 # C4H C4H
pair_coeff 1 2 lj/cut/coul/long 0.0445 2.9580 # C4H H
pair_coeff 2 2 lj/cut/coul/long 0.0300 2.5000 # H H
pair_coeff 3 3 lj/cut/tip4p/long/soft 0.1628 3.1644 1.0 # Ow Ow
pair_coeff 3 4 lj/cut/tip4p/long/soft 0.0000 1.0000 1.0 # Ow Hw
pair_coeff 4 4 lj/cut/tip4p/long/soft 0.0000 1.0000 1.0 # Hw Hw
pair_coeff 1 3 lj/cut/tip4p/long/soft 0.1036 3.3279 0.0 # C4H Ow
pair_coeff 1 4 lj/cut/tip4p/long/soft 0.0000 1.0000 0.0 # C4H Hw
pair_coeff 2 3 lj/cut/tip4p/long/soft 0.0699 2.8126 0.0 # H Ow
pair_coeff 2 4 lj/cut/tip4p/long/soft 0.0000 1.0000 0.0 # H Hw
variable nsteps equal 2500000
variable nprint equal ${nsteps}/500
variable ndump equal ${nsteps}/100
variable temp equal 300.0
variable press equal 1.0
fix fSHAKE all shake 0.0001 20 ${nprint} b 2 a 2
neighbor 2.0 bin
timestep 2.0
# velocity all create ${temp} 12345
thermo_style multi
thermo ${nprint}
fix fNPT all npt temp ${temp} ${temp} 100 iso ${press} ${press} 1000
run 250000
reset_timestep 0
variable lambda equal ramp(0.0,1.0)
fix fADAPT all adapt/fep 125000 pair lj/cut/tip4p/long/soft lambda 1*2 3*4 v_lambda after yes
variable dlambda equal 0.05
compute cFEP all fep ${temp} pair lj/cut/tip4p/long/soft lambda 1*2 3*4 v_dlambda
fix fFEP all ave/time 25 4000 125000 c_cFEP[1] c_cFEP[2] file fep01.lmp
# compute cRDF all rdf 100 3 3 3 4 4 4
# fix fRDF all ave/time 2000 500 ${nsteps} c_cRDF file rdf.lammps mode vector
group owater type 3
compute cMSD owater msd
fix fMSD owater ave/time 1 1 ${ndump} c_cMSD[1] c_cMSD[2] c_cMSD[3] c_cMSD[4] file msd.lammps
dump dCONF all custom ${ndump} dump.lammpstrj id mol type element x y z ix iy iz
dump_modify dCONF element C H O H
run ${nsteps}
# write_restart restart.*.lmp
write_data data.*.lmp
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