# chitosan units real #boundary p p p variable sys_name string water variable run string test.nvt log ${sys_name}.${run}.log atom_style full read_data ${sys_name}.data # * k length bond_style harmonic bond_coeff 1 59.75 1.400 # polarizable PW W-WP, W-WM 50000 in kJ # * k theta angle_style hybrid harmonic cosine/squared angle_coeff 1 cosine/squared 0.50 0.0 # polarizable PW WP-W-WM 4.2 in kJ # * inner outer pair_style lj/cut/coul/long 16 kspace_style pppm 7e-5 kspace_modify mesh 1 1 1 order 4 force 7.0e-5 pair_coeff 1 1 0.965 4.7 pair_coeff 2 2 0 0 pair_coeff 3 3 0 0 pair_coeff 1 2 0 0 pair_coeff 1 3 0 0 pair_coeff 2 3 0 0 # 1-2, 1-3, 1-4 exclusions special_bonds lj 0.0 0.0 0.0 coul 0.0 0.0 0.0 dielectric 2.5 neighbor 2.0 bin # this many angstrom beyond force cutoff 16A neigh_modify every 1 delay 0 check yes # build every this many steps group PW type 1 2 3 group test_pw id 2 3 ###### END OF HEADER ###### velocity all create 300 935127 thermo_style multi #thermo_style custom temp emol epair ecoul elong etotal thermo 100 timestep 10 run_style verlet compute T all temp compute P all pressure T compute B test_pw pair/local dist eng force dump C test_pw local 1 water.dump index c_B[1] c_B[2] c_B[3] fix 1 PW shake 1.0e-8 1000 0 b 1 fix 3 PW nvt temp 300 300 $(100.0*dt) run 10000