02_water_aa.in.run

# Derived variables.
variable d       equal $p*$s        # thermo interval
variable dcycle  equal $d            # dump interval (same as thermo)
variable tcouple equal ${ts}*100   # Coupling constant for Temperature
variable pcouple equal ${ts}*1000  # Coupling constant for Pressure.

# Create a random seed.
shell dd if=/dev/urandom of=/tmp/random_number count=2 bs=1
shell od -An --format=dI /tmp/random_number > /tmp/seed
variable s1 file /tmp/seed
variable s2 equal abs(v_s1)
print "Random Seed ${s2}"
variable r1 equal random(10000,1000000,${s2})

# Output.
thermo       $d
thermo_style custom step etotal evdwl ecoul elong ebond ke pe temp press pxx pyy pzz vol density cpu    
thermo_modify flush yes
dump 1 all dcd $d ${run}.dcd 
dump_modify 1 unwrap yes

# 1. Equilibrate the sample.
timestep        ${ts}
velocity        all create ${temp} 391624 dist gaussian
fix             1 all shake .0001 10 0 m 1.0079 a 1
fix             2 all nph iso 1. 1. ${pcouple}
variable r format r1 %.0f
fix             3 all langevin ${temp} ${temp} ${tcouple} $r
run   ${equi}