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lammps/examples/USER/fep/CC-CO/fep01/in.fep01
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in.fep01
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# created by fftool
units real
boundary p p p
atom_style full
bond_style harmonic
angle_style harmonic
dihedral_style opls
special_bonds lj/coul 0.0 0.0 0.5
read_data data.0.lmp
# read_restart restart.*.lmp
# reset_timestep 0
pair_style hybrid lj/cut/coul/long 10.0 10.0 &
lj/cut/coul/long/soft 1 0.5 10.0 10.0 10.0
pair_modify tail no
kspace_style pppm 1.0e-4
pair_coeff 1 1 none # C-CO C-CO
pair_coeff 1 2 none # C-CO C-D
pair_coeff 1 3 none # C-CO H-D
pair_coeff 1 4 none # C-CO H-H1
pair_coeff 1 5 none # C-CO OHD-
pair_coeff 1 6 none # C-CO HOD-
pair_coeff 1 7 lj/cut/coul/long 0.0000 1.0000 # C-CO Hw
pair_coeff 1 8 lj/cut/coul/long 0.1013 3.3286 # C-CO Ow
pair_coeff 2 2 none # C-D C-D
pair_coeff 2 3 none # C-D H-D
pair_coeff 2 4 none # C-D H-H1
pair_coeff 2 5 none # C-D OHD-
pair_coeff 2 6 none # C-D HOD-
pair_coeff 2 7 lj/cut/coul/long/soft 0.0000 1.0000 1.0 # C-D Hw
pair_coeff 2 8 lj/cut/coul/long/soft 0.1013 3.3286 1.0 # C-D Ow
pair_coeff 3 3 none # H-D H-D
pair_coeff 3 4 lj/cut/coul/long/soft 0.0300 2.5000 1.0 # H-D H-H1
pair_coeff 3 5 none # H-D OHD-
pair_coeff 3 6 none # H-D HOD-
pair_coeff 3 7 lj/cut/coul/long/soft 0.0000 1.0000 1.0 # H-D Hw
pair_coeff 3 8 lj/cut/coul/long/soft 0.0683 2.8131 1.0 # H-D Ow
pair_coeff 4 4 none # H-H1 H-H1
pair_coeff 4 5 none # H-H1 OHD-
pair_coeff 4 6 lj/cut/coul/long/soft 0.0000 1.0000 0.0 # H-H1 HOD-
pair_coeff 4 7 lj/cut/coul/long 0.0000 1.0000 # H-H1 Hw
pair_coeff 4 8 lj/cut/coul/long 0.0683 2.8131 # H-H1 Ow
pair_coeff 5 5 none # OHD- OHD-
pair_coeff 5 6 none # OHD- HOD-
pair_coeff 5 7 lj/cut/coul/long/soft 0.0000 1.0000 0.0 # OHD- Hw
pair_coeff 5 8 lj/cut/coul/long/soft 0.1625 3.1427 0.0 # OHD- Ow
pair_coeff 6 6 none # HOD- HOD-
pair_coeff 6 7 lj/cut/coul/long/soft 0.0000 1.0000 0.0 # HOD- Hw
pair_coeff 6 8 lj/cut/coul/long/soft 0.0000 1.7792 0.0 # HOD- Ow
pair_coeff 7 7 lj/cut/coul/long 0.0000 1.0000 # Hw Hw
pair_coeff 7 8 lj/cut/coul/long 0.0000 1.0000 # Hw Ow
pair_coeff 8 8 lj/cut/coul/long 0.1554 3.1655 # Ow Ow
variable nsteps equal 25000
variable nprint equal ${nsteps}/500
variable ndump equal ${nsteps}/100
# variable nrestart equal ${nsteps}/10
variable temp equal 300.0
variable press equal 1.0
neighbor 2.0 bin
timestep 2.0
# velocity all create ${temp} 12345
thermo_style multi
thermo ${nprint}
fix fSHAKE all shake 0.0001 20 ${nprint} b 2 4 5 a 6
fix fNPT all npt temp ${temp} ${temp} 100 iso ${press} ${press} 500
run 10000
reset_timestep 0
write_restart init.restart
variable lambda equal ramp(0.0,1.0)
variable minusl equal 1.0-v_lambda
variable q1 equal 0.145*v_lambda-0.180*(1.0-v_lambda)
variable q2 equal -0.180*(1.0-v_lambda)
variable q3 equal 0.060*(1.0-v_lambda)
variable q4 equal 0.040*v_lambda+0.060*(1.0-v_lambda)
variable q5 equal -0.683*v_lambda
variable q6 equal 0.418*v_lambda
fix fADAPT all adapt/fep 125000 &
pair lj/cut/coul/long/soft lambda 2*3 7*8 v_minusl &
pair lj/cut/coul/long/soft lambda 3 4 v_minusl &
pair lj/cut/coul/long/soft lambda 4 6 v_lambda &
pair lj/cut/coul/long/soft lambda 5*6 7*8 v_lambda &
atom charge 1 v_q1 &
atom charge 2 v_q2 &
atom charge 3 v_q3 &
atom charge 4 v_q4 &
atom charge 5 v_q5 &
atom charge 6 v_q6 &
after yes
variable dlambda equal 0.05
variable minusdl equal -0.05
variable dq1 equal 0.145*v_dlambda+0.180*v_dlambda
variable dq2 equal 0.180*v_dlambda
variable dq3 equal -0.060*v_dlambda
variable dq4 equal 0.040*v_dlambda-0.060*v_dlambda
variable dq5 equal -0.683*v_dlambda
variable dq6 equal 0.418*v_dlambda
compute cFEP all fep ${temp} &
pair lj/cut/coul/long/soft lambda 2*3 7*8 v_minusdl &
pair lj/cut/coul/long/soft lambda 3 4 v_minusdl &
pair lj/cut/coul/long/soft lambda 4 6 v_dlambda &
pair lj/cut/coul/long/soft lambda 5*6 7*8 v_dlambda &
atom charge 1 v_dq1 &
atom charge 2 v_dq2 &
atom charge 3 v_dq3 &
atom charge 4 v_dq4 &
atom charge 5 v_dq5 &
atom charge 6 v_dq6
fix fFEP all ave/time 25 4000 125000 c_cFEP[1] c_cFEP[2] file fep01.lmp
# compute cRDF all rdf 100 1 1
# fix fRDF all ave/time 20 100 ${nsteps} c_cRDF file rdf.lammps mode vector
compute cMSD all msd
fix fMSD all 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 C H H O H H O
# restart ${nrestart} restart.*.lmp
run ${nsteps}
write_restart restart.*.lmp
write_data data.*.lmp
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