GROMACS topology file for the TIP4P/Ice model: Difference between revisions

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(New page: 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 ...)
 
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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 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
The following is a topology file for the [[TIP4P/Ice]] model of [[water]] for use in the [[GROMACS]] computer simulation package.  




[ 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]
[moleculetype]
  ; name nrexcl
; name nrexcl
  water  1
water  1
 
 
  [atoms]
[atoms]
  ; nr type resnr residu atom cgnr charge
; nr type resnr residu atom cgnr charge
  1    OWT4 1    water  OW1  1    0          15.994
1    OWT4 1    water  OW1  1    0          15.994
  2    HW  1    water  HW2  1    0.5897    1.008
2    HW  1    water  HW2  1    0.5897    1.008
  3    HW  1    water  HW3  1    0.5897    1.008
3    HW  1    water  HW3  1    0.5897    1.008
  4    IW  1    water  MW4  1    -1.1794    0.0
4    IW  1    water  MW4  1    -1.1794    0.0
 
 
  [constraints]
[constraints]
  ;i j funct doh  dhh
;i j funct doh  dhh
  1      2      1      0.09572
1      2      1      0.09572
  1      3      1      0.09572
1      3      1      0.09572
  2      3      1      0.15139
2      3      1      0.15139
 
 
  [exclusions]
[exclusions]
  1      2      3      4
1      2      3      4
  2      1      3       4
2      1      2       3
  3      1      2      4
3      1      2      4
  4      1      2      3
4      1      2      3
 
 
  ; The position of the dummy is computed as follows:
 
  ;
; The position of the dummy is computed as follows:
  ;              O
;
  ;
;              O
  ;               D
;
  ;
;               D
  ;      H              H
;
  ;
;      H              H
  ; const = distance (OD) / [ cos (angle(DOH))    * distance (OH) ]
;
  ;        0.015 nm      / [ cos (52.26 deg)    * 0.09572 nm    ]
; const = distance (OD) / [ cos (angle(DOH))    * distance (OH) ]
  ; Dummy pos x4 = x1 + a*(x2-x1) + b*(x3-x1)
;        0.015 nm      / [ cos (52.26 deg)    * 0.09572 nm    ]
 
 
  [dummies3]
; Dummy pos x4 = x1 + a*(x2-x1) + b*(x3-x1)
  ; Dummy from                    funct  a              b
 
  4      1      2      3      1      0.13458        0.13458
 
 
[dummies3]
  [system]
; Dummy from                    funct  a              b
  water TIP4P/Ice
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]]

Latest revision as of 15:26, 25 May 2021

The following is a topology file for the TIP4P/Ice model of water for use in the GROMACS computer simulation package.


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