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##########################
#  Initialization
#-------------------------
boundary        p p p
units           real

#------------------------------
# Force field specifications
#------------------------------
atom_style      full
bond_style      harmonic
angle_style     charmm
dihedral_style  charmm
pair_style      lj/charmm/coul/charmm 10 12
pair_modify     mix arithmetic
neigh_modify    every 2 delay 10 check yes
special_bonds   charmm

#----------------
# Read geometry
#----------------
read_data       solved_d10.data

#---------------------
# Define Groups
#---------------------
group           water     type 1 10
group           wato      type 10
group           allsulfur type 7
group           uppersurf molecule <> 49 96
group           lowersurf molecule <> 1  48
group           uppersulfur    intersect allsulfur uppersurf
group           lowersulfur    intersect allsulfur lowersurf
group           uppernosulfur  subtract  uppersurf uppersulfur
group           lowernosulfur  subtract  lowersurf lowersulfur
group           pControl       union     lowernosulfur uppernosulfur water
group           twosurfs       union     lowersurf uppersurf

#---------------------
# Fix all sulfur atoms
#---------------------
fix                 fixsulfur allsulfur setforce 0.0 0.0 0.0

#--------------
# Minimization
#--------------
min_style       sd
minimize        0.0 1.0e-8 1000 100000

#-----------------------
# Initialize velocities
#-----------------------
velocity         all create 10.0 4928459 rot yes mom yes dist gaussian

#---------------------
# Shake all H atoms
#---------------------
fix                 shakeH all shake 0.0001 20 0 m 1.0 a 11

#---------------------
## Set Shear Velocity
##---------------------
variable        xu equal vdisplace(0.0,0.0001)
variable        xl equal vdisplace(0.0,-0.0001)
fix                vu uppersurf move variable v_xu NULL NULL NULL NULL NULL
fix                vl lowersurf move variable v_xl NULL NULL NULL NULL NULL

#--------------------------------
# Define the integration method
#--------------------------------
fix                1  all npt temp 10.0 300.0 100.0 z 1.0 1.0 1000.0

#-------------------------------
# Customize output infomration
#-------------------------------
thermo          10000  
thermo_style    multi
dump                mydump  all atom 10000 trjequil.lammpstrj   
restart         500000  res.equil                           

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3Â¥: Originally posted by lx_PICO at 2015-05-21 15:23:24
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4Â¥: Originally posted by Ace_xt at 2015-05-21 17:49:19
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Ace_xt

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5Â¥: Originally posted by lx_PICO at 2015-05-21 20:18:41
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6Â¥: Originally posted by Ace_xt at 2015-05-21 21:53:07
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