[gmx-users] atomtypes, parameters in file do not match parameters in manual

[Mark Abraham]

Andreas Kring wrote:
> Hello all.
> 
> I'm new to Gromacs, so sorry for this (probably naive) question:
> 
> In Table 5.3 in the Gromacs manual version 3.3, the parameters for 
> [atomtypes] are: atom type, mass, charge, particle type, V and W.
> 
> In the Gromacs directory containing the the force fields 
> (/usr/local/gromacs/share/gromacs/top on my machine) the ffoplsaanb.itp 
> file begins with the following lines:
> 
> [ atomtypes ]
> ; full atom descriptions are available in ffoplsaa.atp
> ; name  bond_type    mass    charge   ptype          sigma      epsilon
>  opls_001   C   6      12.01100     0.500       A    3.75000e-01 
> 4.39320e-01 ; SIG
> 
> Why do the manual parameters not match the parameters in the file?
> Which of the two are correct?

There's an undocumented feature where the fields in an [ atomtypes ] 
line follow one of several possible formats and grompp is smart about 
working one which field means what.

Mark