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simongravellesimongravelle
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Merge pull request #23 from lammpstutorials/continue-improving-tutorial-3
continue improving tutorial 3
2 parents 7f31b87 + 0d08d30 commit ed3adc9

6 files changed

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files/tutorial3/PEG-GROMOS.mol renamed to files/tutorial3/mergePEGH2O/PEG-GROMOS.mol

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‎files/tutorial3/mergePEGH2O/input.lmp‎

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units real
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atom_style full
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bond_style harmonic
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angle_style harmonic
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dihedral_style harmonic
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pair_style lj/cut/coul/long 10
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kspace_style pppm 1e-5
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special_bonds lj 0.0 0.0 0.5 coul 0.0 0.0 1.0 &
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angle yes dihedral yes
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read_data ../pureH2O/H2O.data &
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extra/bond/per/atom 3 &
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extra/angle/per/atom 6 &
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extra/dihedral/per/atom 10 &
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extra/special/per/atom 14
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include ../PARM.lmp
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molecule pegmol PEG-GROMOS.mol
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create_atoms 0 single 0 0 0 mol pegmol 454756
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group H2O type OW HW
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group PEG type C CPos H HC OAlc OE
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delete_atoms overlap 2.0 H2O PEG mol yes
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fix mynpt all npt temp 300 300 100 x 1 1 1000
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timestep 1.0
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dump mydmp all image 1000 dump.*.ppn type &
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type shiny 0.1 box no 0.01 &
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view 0 90 zoom 1.8 fsaa yes bond atom 0.8
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dump_modify mydmp backcolor white &
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acolor OW red acolor HW white &
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acolor OE red acolor OAlc red &
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acolor C gray acolor CPos gray &
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acolor H white acolor HC white &
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adiam OW 0.2 adiam HW 0.2 &
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adiam C 3 adiam CPos 3 adiam OAlc 2.8 &
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adiam H 1 adiam HC 1 adiam OE 2.8
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thermo 1000
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run 30000
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write_data mix.data

‎files/tutorial3/pullonPEG/input.lmp‎

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variable f0 equal 5
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units real
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atom_style full
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bond_style harmonic
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angle_style harmonic
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dihedral_style harmonic
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pair_style lj/cut/coul/long 10
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kspace_style pppm 1e-5
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special_bonds lj 0.0 0.0 0.5 &
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coul 0.0 0.0 1.0 &
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angle yes dihedral yes
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read_data ../mergePEGH2O/mix.data
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include ../PARM.lmp
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group H2O type OW HW
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group PEG type C CPos H HC OAlc OE
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group ends type OAlc
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variable xcm equal xcm(ends,x)
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variable oxies atom type==label2type(atom,OAlc)
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variable end1 atom v_oxies*(x>v_xcm)
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variable end2 atom v_oxies*(x<v_xcm)
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group topull1 variable end1
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group topull2 variable end2
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dump mydmp all image 1000 dump.*.ppn type &
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type shiny 0.1 box no 0.01 &
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view 0 90 zoom 1.8 fsaa yes bond atom 0.8
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dump_modify mydmp backcolor white &
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acolor OW red acolor HW white &
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acolor OE red acolor OAlc red &
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acolor C gray acolor CPos gray &
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acolor H white acolor HC white &
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adiam OW 0.2 adiam HW 0.2 &
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adiam C 3 adiam CPos 3 adiam OAlc 2.8 &
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adiam H 1 adiam HC 1 adiam OE 2.8
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variable x1 equal xcm(topull1,x)
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variable x2 equal xcm(topull2,x)
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variable y1 equal xcm(topull1,y)
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variable y2 equal xcm(topull2,y)
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variable z1 equal xcm(topull1,z)
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variable z2 equal xcm(topull2,z)
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variable delta_r equal sqrt((v_x1-v_x2)^2+(v_y1-v_y2)^2+(v_z1-v_z2)^2)
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compute rgyr PEG gyration
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thermo_style custom step temp etotal v_delta_r c_rgyr
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thermo 1000
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timestep 1.0
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fix mynvt all nvt temp 300 300 100
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run 30000
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fix myaf1 topull1 addforce ${f0} 0 0
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fix myaf2 topull2 addforce -${f0} 0 0
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run 30000

files/tutorial3/H2O-SPCFw.mol renamed to files/tutorial3/pureH2O/H2O-SPCFw.mol

File renamed without changes.

‎files/tutorial3/pureH2O/input.lmp‎

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units real
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atom_style full
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bond_style harmonic
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angle_style harmonic
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dihedral_style harmonic
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pair_style lj/cut/coul/long 10
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kspace_style pppm 1e-5
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special_bonds lj 0.0 0.0 0.5 &
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coul 0.0 0.0 1.0 angle yes
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region box block -45 45 -15 15 -15 15
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create_box 8 box &
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bond/types 7 &
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angle/types 8 &
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dihedral/types 4 &
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extra/bond/per/atom 3 &
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extra/angle/per/atom 6 &
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extra/dihedral/per/atom 10 &
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extra/special/per/atom 14
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include ../PARM.lmp
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molecule h2omol H2O-SPCFw.mol
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create_atoms 0 random 1050 87910 NULL mol &
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h2omol 454756 overlap 1.0 maxtry 50
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group H2O type OW HW
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minimize 1.0e-4 1.0e-6 100 1000
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reset_timestep 0
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fix mynpt all npt temp 300 300 100 &
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iso 1 1 1000
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dump mydmp all image 500 dump.*.jpg type type &
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shiny 0.1 box no 0.01 view 0 90 zoom 1.8
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dump_modify mydmp backcolor white &
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acolor OW red acolor HW white &
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adiam OW 3 adiam HW 1.5
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variable myvol equal vol
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variable myoxy equal count(H2O)/3
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variable rho equal ${myoxy}/v_myvol
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thermo 1000
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thermo_style custom step temp etotal v_myvol v_rho
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timestep 1.0
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run 20000
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write_data H2O.data

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