# Created by charmm2lammps v1.9.1 on Mon 13 Dec 2021 12:44:15 AM +0330 # Command: charmm2lammps.pl all27_prot_lipid water1_autopsf echo both units real boundary p p p neigh_modify delay 2 every 1 timestep 1 atom_style full bond_style harmonic angle_style harmonic read_data solvate.data bond_coeff 1 469.0 1.0 #H-O bond_coeff 2 450.0 1.418 #C-C angle_coeff 1 85.0 109.47 #H-O-H set type 1 charge 0.4238 set type 2 charge -0.8476 pair_style hybrid lj/charmm/coul/long 8 10 tersoff pair_coeff * * tersoff SiC_real.tersoff NULL NULL C #C-C pair_coeff 1 1 lj/charmm/coul/long 0.046 0.400013524445 # H-H pair_coeff 2 2 lj/charmm/coul/long 0.1521 3.15057422683 # O-O pair_coeff 1 2 lj/charmm/coul/long 0.0836 1.7753 # H-O pair_coeff 1 3 lj/charmm/coul/long 0.0567 1.9750 # H-C pair_coeff 2 3 lj/charmm/coul/long 0.1032 3.503 # O-C #pair_style lj/charmm/coul/long 8.0 10.0 #pair_coeff 1 1 0.0 0.0 #H-H #pair_coeff 2 2 0.1553 3.166 #O-O #pair_coeff 3 3 0.07 3.9848 #C-C #pair_coeff 1 2 0.0 0.0 #H-O #pair_coeff 1 3 0.0 1.9924 #H-C #pair_coeff 2 3 0.104264 3.5754 #O-C kspace_style pppm 1e-4 neighbor 2 bin neigh_modify exclude type 3 3 neigh_modify delay 0 every 1 check yes min_style cg minimize 1.0e-4 1.0e-6 100 1000 group solvent type 1 2 group cnt type 3 velocity solvent create 298.0 12345678 dist uniform #Apply Nose-Hoover termostate on water molecules delete_atoms overlap 0.3 solvent cnt mol yes compute mytemp all temp #solvent fix 3 all nvt temp 298.0 298.0 100 fix_modify 3 temp mytemp fix push cnt nve velocity cnt set 0 0 0 units box fix NOFORCE1 cnt setforce 0 0 0 region trash cylinder z 20 20 7.54 1 41 units box side out #7.84 delete_atoms region trash bond yes thermo 1000 thermo_style custom step press temp c_mytemp pe ke etotal log logequi.txt thermo_modify temp mytemp dump 1 all custom 1000 dump.lammpstrj id type x y z write_data output.data run 100000 # 100000 undump 1 reset_timestep 0 ############################################## Pressure Tensor####################### group solvent type 1 2 region cntube cylinder z 20 20 6.77 1 41 units box #compute mytemp solvent temp #fix 3 solvent nvt temp 298.0 298.0 100 #fix_modify 3 temp mytemp #thermo_modify temp mytemp compute vis solvent stress/atom mytemp compute visco solvent reduce sum c_vis[1] c_vis[2] c_vis[3] & c_vis[4] c_vis[5] c_vis[6] variable pxxcyl equal -(c_visco[1])/(3*5759.532077) variable pyycyl equal -(c_visco[2])/(3*5759.532077) variable pzzcyl equal -(c_visco[3])/(3*5759.532077) variable pxycyl equal -(c_visco[4])/(3*5759.532077) variable pxzcyl equal -(c_visco[5])/(3*5759.532077) variable pyzcyl equal -(c_visco[6])/(3*5759.532077) group oxyg type 2 variable Countcyl equal count(oxyg,cntube) ##################################################################### variable p equal 20 #Correlation Length variable s equal 5 #sample interval variable d equal $p*$s #dump interval # Convert from LAMMPS real units to SI variable kB equal 1.3806504e-23 #[J/K] Boltzmann variable atm2Pa equal 101325.0 variable A2m equal 1.0e-10 variable fs2s equal 1.0e-15 variable convert equal ${atm2Pa}*${atm2Pa}*${fs2s}*${A2m}*${A2m}*${A2m} variable pxy equal pxy variable pxz equal pxz variable pyz equal pyz variable pxx equal pxx #pxx variable pyy equal pyy #pyy variable pzz equal pzz #pzz fix SS all ave/correlate $s $p $d & v_pxy v_pxz v_pyz v_pxx v_pyy v_pzz type auto file S0St.dat ave running variable T equal 298 variable vol equal 5759.5320 variable dt equal 1 variable scale equal ${convert}/(${kB}*$T)*${vol}*$s*${dt} variable v11 equal trap(f_SS[3])*${scale} variable v22 equal trap(f_SS[4])*${scale} variable v33 equal trap(f_SS[5])*${scale} variable v1122 equal trap(f_SS[6]-f_SS[7])*${scale} variable v2233 equal trap(f_SS[7]-f_SS[8])*${scale} variable v equal (v_v11+v_v22+v_v33+v_v1122+v_v2233)/5.0 thermo 1000 thermo_style custom step press temp v_v v_pxxcyl v_pyycyl v_pzzcyl v_pxycyl & v_pxzcyl v_pyzcyl v_Countcyl log logequi2.txt #thermo_modify press vis thermo_modify temp mytemp dump 2 all custom 10000 dump2.lammpstrj id type x y z run 100000 # 100000