[gmx-users] .gro => atom number

[Mark Abraham]

Chih-Ying Lin wrote:
> Hi
> 
> .gro file
> 
> MD of 2 waters, t= 0.0
> 6
>     1ABC OW1    1   0.126   1.624   1.679  0.1227 -0.0580  0.0434
>     1ABC HW2    2   0.190   1.661   1.747  0.8085  0.3191 -0.7791
>     1ABC HW3    3   0.177   1.568   1.613 -0.9045 -2.6469  1.3180
>     2ABC OW1    4   1.275   0.053   0.622  0.2519  0.3140 -0.1734
>     2ABC HW2    5   1.337   0.002   0.680 -1.0641 -1.1349  0.0257
>     2ABC HW3    6   1.326   0.120   0.568  1.9427 -0.8216 -0.0244
>    1.82060   1.82060   1.82060
> 
>                         ^
>                         ||
>    atom number (5 positions, integer)
> 
> 
> Since .top only define the force field by the atom number set (1,2,3).
> 
> 
> Should this atom number set become =>
> 1                           1
> 2                           2
> 3        =>               3
> 4                           1
> 5                           2
> 6                           3

A .top and a coordinate file only have to make sense together when 
interpreted by grompp. The first requirement is that the order of the 
molecules match the order implied in the .top [molecules] section. 
Within each molecule the atom numbering needs to be increasing (IIRC, 
but not uniformly increasing) and the atom names must match in order.

The necessary conditions for pdb2gmx to produce a topology from a 
coordinate file are broadly similar but use different pieces of information.

Mark