top file format

Main Table of Contents VERSION 5.0.3

Description

The top file extension stands for topology. It is an ascii file which is read by gmx grompp which processes it and creates a binary topology (.tpb file).
A sample file is included below:
;
;	Example topology file
;
[ defaults ]
; nbfunc        comb-rule       gen-pairs       fudgeLJ fudgeQQ
  1             1               no              1.0     1.0

; The force field files to be included
#include "rt41c5.itp"	

[ moleculetype ]
; name  nrexcl
Urea         3

[ atoms ]
;   nr    type   resnr  residu    atom    cgnr  charge
     1       C       1    UREA      C1       1	 0.683	
     2       O       1    UREA      O2       1	-0.683
     3      NT       1    UREA      N3       2	-0.622
     4       H       1    UREA      H4       2	 0.346
     5       H       1    UREA      H5       2	 0.276
     6      NT       1    UREA      N6       3	-0.622
     7       H       1    UREA      H7       3   0.346
     8       H       1    UREA      H8       3	 0.276

[ bonds ]
;  ai    aj funct           c0           c1
    3     4     1 1.000000e-01 3.744680e+05 
    3     5     1 1.000000e-01 3.744680e+05 
    6     7     1 1.000000e-01 3.744680e+05 
    6     8     1 1.000000e-01 3.744680e+05 
    1     2     1 1.230000e-01 5.020800e+05 
    1     3     1 1.330000e-01 3.765600e+05 
    1     6     1 1.330000e-01 3.765600e+05 

[ pairs ]
;  ai    aj funct           c0           c1
    2     4     1 0.000000e+00 0.000000e+00 
    2     5     1 0.000000e+00 0.000000e+00 
    2     7     1 0.000000e+00 0.000000e+00 
    2     8     1 0.000000e+00 0.000000e+00 
    3     7     1 0.000000e+00 0.000000e+00 
    3     8     1 0.000000e+00 0.000000e+00 
    4     6     1 0.000000e+00 0.000000e+00 
    5     6     1 0.000000e+00 0.000000e+00 

[ angles ]
;  ai    aj    ak funct           c0           c1
    1     3     4     1 1.200000e+02 2.928800e+02 
    1     3     5     1 1.200000e+02 2.928800e+02 
    4     3     5     1 1.200000e+02 3.347200e+02 
    1     6     7     1 1.200000e+02 2.928800e+02 
    1     6     8     1 1.200000e+02 2.928800e+02 
    7     6     8     1 1.200000e+02 3.347200e+02 
    2     1     3     1 1.215000e+02 5.020800e+02 
    2     1     6     1 1.215000e+02 5.020800e+02 
    3     1     6     1 1.170000e+02 5.020800e+02 

[ dihedrals ]
;  ai    aj    ak    al funct           c0           c1           c2
    2     1     3     4     1 1.800000e+02 3.347200e+01 2.000000e+00 
    6     1     3     4     1 1.800000e+02 3.347200e+01 2.000000e+00 
    2     1     3     5     1 1.800000e+02 3.347200e+01 2.000000e+00 
    6     1     3     5     1 1.800000e+02 3.347200e+01 2.000000e+00 
    2     1     6     7     1 1.800000e+02 3.347200e+01 2.000000e+00 
    3     1     6     7     1 1.800000e+02 3.347200e+01 2.000000e+00 
    2     1     6     8     1 1.800000e+02 3.347200e+01 2.000000e+00 
    3     1     6     8     1 1.800000e+02 3.347200e+01 2.000000e+00 

[ dihedrals ]
;  ai    aj    ak    al funct           c0           c1
    3     4     5     1     2 0.000000e+00 1.673600e+02 
    6     7     8     1     2 0.000000e+00 1.673600e+02 
    1     3     6     2     2 0.000000e+00 1.673600e+02 

; Include SPC water topology
#include "spc.itp"

[ system ]
Urea in Water

[ molecules ]
Urea	1
SOL	1000


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