inputformat
'Towhee'
ensemble
'nvt'
temperature
400.0d0
nmolty
6
nmolectyp
1 1 1 1 1 1
numboxes
1
stepstyle
'cycles'
nstep
10
printfreq 
1
blocksize 
2
moviefreq
100000
backupfreq  
1000
runoutput
'full'
pdb_output_freq
100000
pressurefreq
20
trmaxdispfreq
1000
volmaxdispfreq
1000
potentialstyle
'internal'
ffnumber
1
ff_filename
/towheebase/ForceFields/towhee_ff_TraPPE-UA
classical_potential
'Lennard-Jones'       
classical_mixrule
'Lorentz-Berthelot'
lshift
.false.
ltailc
.true.
rmin  
1.0d0 
rcut  
14.0d0
rcutin 
5.0d0 
electrostatic_form
'coulomb'
coulombstyle
'ewald_fixed_kmax'
kalp
5.6d0
kmax
5
dielect
1.0d0
linit   
.true.
initboxtype
'dimensions'
initstyle
'full cbmc' 'full cbmc' 'full cbmc' 'full cbmc' 'full cbmc' 'full cbmc' 
initlattice
'simple cubic' 'simple cubic' 'simple cubic' 'simple cubic' 'simple cubic' 'simple cubic' 
initmol
1 1 1 1 1 1
inix iniy iniz
2    3    1
hmatrix
40.0d0 0.0d0 0.0d0
0.0d0 40.0d0 0.0d0
0.0d0 0.0d0 40.0d0
pm1boxcomswitch
0.1d0     
          pm1comswbox
          1.0d0
          pm1comswpair
          0.07d0 0.13d0 0.20d0 0.27d0 0.33d0 0.40d0 0.47d0 0.53d0 0.60d0 0.67d0 0.73d0 0.80d0 0.87d0 0.93d0 1.0d0
pmcb      
0.25d0     
          pmcbmt
          0.166d0 0.333d0 0.5d0 0.666d0 0.833d0 1.0d0
          pmall
          0.0d0 0.0d0 0.0d0 0.0d0 0.0d0 0.0d0
pmcomposite   
0.50d0	  
          pmcomt
          0.166d0 0.333d0 0.5d0 0.666d0 0.833d0 1.0d0
          rmcomtra
          10.0d0 
          rmcomrot
          1.0d0
pmtracm   
0.75d0	  
          pmtcmt
          0.166d0 0.333d0 0.5d0 0.666d0 0.833d0 1.0d0
          rmtrac
          0.5d0 
          tatrac
          0.5d0
pmrotate
1.0d0
          pmromt  
          0.166d0 0.333d0 0.5d0 0.666d0 0.833d0 1.0d0
          rmrot
          0.05d0
          tarot
          0.5d0
#(3-ethylpentane)
input_style
'basic connectivity map'
nunit
16
nmaxcbmc
16
lpdbnames
F
forcefield
'TraPPE-UA'
charge_assignment
'bond increment'
unit ntype
1    'CH3*(sp3)'
vibration
1
2
improper torsion
0
unit ntype
2    'Ccccc(sp3)'
vibration
4
1 3 10 11
improper torsion
0
unit ntype
3    'CH2**(sp3)'
vibration
2
2 4
improper torsion
0
unit ntype
4    'Ccccc(sp3)'
vibration
4
3 5 12 13
improper torsion
0
unit ntype
5    'CH2**(sp3)'
vibration
2
4 6
improper torsion
0
unit ntype
6    'CHccc(sp3)'
vibration
3
5 7 14
improper torsion
0
unit ntype
7    'CH2**(sp3)'
vibration
2
6 8
improper torsion
0
unit ntype
8    'Ccccc(sp3)'
vibration
4
7 9 15 16
improper torsion
0
unit ntype
9    'CH3*(sp3)'
vibration
1
8
improper torsion
0
unit ntype
10    'CH3*(sp3)'
vibration
1
2
improper torsion
0
unit ntype
11    'CH3*(sp3)'
vibration
1
2
improper torsion
0
unit ntype
12    'CH3*(sp3)'
vibration
1
4
improper torsion
0
unit ntype
13    'CH3*(sp3)'
vibration
1
4
improper torsion
0
unit ntype
14    'CH3*(sp3)'
vibration
1
6
improper torsion
0
unit ntype
15    'CH3*(sp3)'
vibration
1
8
improper torsion
0
unit ntype
16    'CH3*(sp3)'
vibration
1
8
improper torsion
0
#(methanol)
input_style
'basic connectivity map'
nunit
3
nmaxcbmc
3
lpdbnames
F
forcefield
'TraPPE-UA'
charge_assignment
'bond increment'
unit ntype
1    'CH3*(sp3)'
vibration
1
2
improper torsion
0
unit ntype
2    'Och(sp3)'
vibration
2
1 3
improper torsion
0
unit ntype
3    'Ho'
vibration
1
2
improper torsion
0
#2,2 dimethylpropanal
input_style
'basic connectivity map'
nunit
6
nmaxcbmc
6
lpdbnames
F
forcefield
'TraPPE-UA'
charge_assignment
'bond increment'
unit ntype
1    'CH3*(sp3)'
vibration
1
2
improper torsion
0
unit ntype
2    'Ccccc(sp3)'
vibration
4
1 3 5 6
improper torsion
0
unit ntype
3    'CHc=o(sp2)'
vibration
2
2 4
improper torsion
0
unit ntype
4    'O=c(sp2)'
vibration
1
3
improper torsion
0
unit ntype
5    'CH3*(sp3)'
vibration
1
2
improper torsion
0
unit ntype
6    'CH3*(sp3)'
vibration
1
2
improper torsion
0
# ether/alcohol
input_style
'basic connectivity map'
nunit
6
nmaxcbmc
6
lpdbnames
F
forcefield
'TraPPE-UA'
charge_assignment
'bond increment'
unit ntype
1    'CH3*(sp3)'
vibration
1
2
improper torsion
0
unit ntype
2    'Occ(sp3)'
vibration
2
1 3
improper torsion
0
unit ntype
3    'CH2**(sp3)'
vibration
2
2 4
improper torsion
0
unit ntype
4    'CH2**(sp3)'
vibration
2
3 5
improper torsion
0
unit ntype
5    'Och(sp3)'
vibration
2
4 6
improper torsion
0
unit ntype
6    'Ho'
vibration
1
5
improper torsion
0
# diol
input_style
'basic connectivity map'
nunit
6
nmaxcbmc
6
lpdbnames
F
forcefield
'TraPPE-UA'
charge_assignment
'bond increment'
unit ntype
1    'Ho'
vibration
1
2
improper torsion
0
unit ntype
2    'Och(sp3)'
vibration
2
1 3
improper torsion
0
unit ntype
3    'CH2**(sp3)'
vibration
2
2 4
improper torsion
0
unit ntype
4    'CH2**(sp3)'
vibration
2
3 5
improper torsion
0
unit ntype
5    'Och(sp3)'
vibration
2
4 6
improper torsion
0
unit ntype
6    'Ho'
vibration
1
5
improper torsion
0
# carboxylic acid
input_style
'basic connectivity map'
nunit
6
nmaxcbmc
6
lpdbnames
F
forcefield
'TraPPE-UA'
charge_assignment
'bond increment'
unit ntype
1    'CH3*(sp3)'
vibration
1
2
improper torsion
0
unit ntype
2    'CH2**(sp3)'
vibration
2
1 3
improper torsion
0
unit ntype
3    'Cco=o(sp2)'
vibration
3
2 4 6
improper torsion
0
unit ntype
4    'Och(sp3)'
vibration
2
3 5
improper torsion
0
unit ntype
5    'Hoacid'
vibration
1
4
improper torsion
0
unit ntype
6    'O=c(sp2)'
vibration
1
3
improper torsion
0

























**** Broken molecules ****

inpstyle molecule (buta-2-one)
2
nunit
8
nmaxcbmc
8
lpdbnames
F
forcefield
'TraPPE-UA'
charge_assignment
'bond increment'
unit ntype
1    'CH3*(sp3)'
vibration
1
2
improper torsion
0
unit ntype
2    'CH2**(sp3)'
vibration
2
1 3
improper torsion
0
unit ntype
3    'Ccc=o(sp2)'
vibration
3
2 4 8
improper torsion
0
unit ntype
4    'Ccccc(sp3)'
vibration
4
3 5 6 7 
improper torsion
0
unit ntype
5    'CH3*(sp3)'
vibration
1
4
improper torsion
0
unit ntype
6    'CH3*(sp3)'
vibration
1
4
improper torsion
0
unit ntype
7    'CH3*(sp3)'
vibration
1
4
improper torsion
0
unit ntype
8    'O=c(sp2)'
vibration
1
3
improper torsion
0
inpstyle molecule (ethyl,2-propyl,ether)
2
nunit
7
nmaxcbmc
7
lpdbnames
F
forcefield
'TraPPE-UA'
charge_assignment
'bond increment'in
unit ntype
1    'CH3*(sp3)'
vibration
1
2
improper torsion
0
unit ntype
2    'CHccc(sp3)'
vibration
3
1 3 6
improper torsion
0
unit ntype
3    'Occ(sp3)'
vibration
2
2 4
improper torsion
0
unit ntype
4    'CH2**(sp3)'
vibration
2
3 5
improper torsion
0
unit ntype
5    'CH3*(sp3)'
vibration
1
4
improper torsion
0
unit ntype
6    'CH2**(sp3)'
vibration
2
2 7
improper torsion
0
unit ntype
7    'CH3*(sp3)'
vibration
1
6
improper torsion
0