Editing GROMACS topology file for the TIP4P/Ice model

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The following is a topology file for the [[TIP4P/Ice]] model of [[water]] for use in the [[GROMACS]] computer simulation package.  
The following is a topology file for the [[TIP4P/ice]] model of [[water]] for use in the [[GROMACS]] computer simulation package. The best way to use this file is to click on the edit tab at the top of this page, and then cut and paste the relevant section in the edit window to the file topol.top




  [ defaults ]
[ defaults ]
  ; nbfunc        comb-rule      gen-pairs      fudgeLJ fudgeQQ
; nbfunc        comb-rule      gen-pairs      fudgeLJ fudgeQQ
   1            2              no              1.0    1.0
   1            2              no              1.0    1.0
 
 
  [atomtypes]
[atomtypes]
  ;name    mass      charge  ptype    sigma        epsilon
;name    mass      charge  ptype    sigma        epsilon
  IW    0            0.000      D  0.0          0.0
IW    0            0.000      D  0.0          0.0
  OWT4  15.99940      0.000      A  0.31668      0.88211
OWT4  15.99940      0.000      A  0.31668      0.88211
  HW    1.00800      0.000      A  0.00000E+00  0.00000E+00
HW    1.00800      0.000      A  0.00000E+00  0.00000E+00
 
 
 
 
  [moleculetype]
 
  ; name nrexcl
[moleculetype]
  water  1
; name nrexcl
 
water  1
  [atoms]
 
  ; nr type resnr residu atom cgnr charge
[atoms]
  1    OWT4 1    water  OW1  1    0          15.994
; nr type resnr residu atom cgnr charge
  2    HW  1    water  HW2  1    0.5897    1.008
1    OWT4 1    water  OW1  1    0          15.994
  3    HW  1    water  HW3  1    0.5897    1.008
2    HW  1    water  HW2  1    0.5897    1.008
  4    IW  1    water  MW4  1    -1.1794    0.0
3    HW  1    water  HW3  1    0.5897    1.008
 
4    IW  1    water  MW4  1    -1.1794    0.0
  [constraints]
 
  ;i j funct doh  dhh
[constraints]
  1      2      1      0.09572
;i j funct doh  dhh
  1      3      1      0.09572
1      2      1      0.09572
  2      3      1      0.15139
1      3      1      0.09572
 
2      3      1      0.15139
  [exclusions]
 
  1      2      3      4
[exclusions]
  2      1      3       4
1      2      3      4
  3      1      2      4
2      1       2       3
  4      1      2      3
3      1      2      4
 
4      1      2      3
  ; The position of the dummy is computed as follows:
 
  ;
 
  ;              O
; The position of the dummy is computed as follows:
  ;
;
  ;               D
;              O
  ;
;
  ;      H              H
;               D
  ;
;
  ; const = distance (OD) / [ cos (angle(DOH))    * distance (OH) ]
;      H              H
  ;        0.015 nm      / [ cos (52.26 deg)    * 0.09572 nm    ]
;
  ; Dummy pos x4 = x1 + a*(x2-x1) + b*(x3-x1)
; const = distance (OD) / [ cos (angle(DOH))    * distance (OH) ]
 
;        0.015 nm      / [ cos (52.26 deg)    * 0.09572 nm    ]
  [dummies3]
 
  ; Dummy from                    funct  a              b
; Dummy pos x4 = x1 + a*(x2-x1) + b*(x3-x1)
  4      1      2      3      1      0.13458        0.13458
 
 
 
  [system]
[dummies3]
  water TIP4P/Ice
; Dummy from                    funct  a              b
 
4      1      2      3      1      0.13458        0.13458
  [molecules]
 
  water  1
 
 
[system]
 
water TIP4P/ice
 
[molecules]
water  1
 
 
 
 


[[category: models]]
[[category: models]]
[[category: water]]
[[category: water]]
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