[gmx-users] water model purpose?

[Mark Abraham]

On 23/11/2010 8:35 PM, ahmet yıldırım wrote:
> Hi,
>
> pdb2gmx -f 1LYD.pdb -water tip3p
>
> Why is -water tip3p command ( tip3p water model) used? What the purpose?

This chooses the water model embedded in the system topology written by 
pdb2gmx.

> Afterwards, genbox command is already added to solvent water as the 
> following:
>
> genbox −cp box.gro −cs spc216.gro −p topol.top −o solvated.gro

This generates the coordinates of the water molecules, but doesn't know 
or care what model the .top employs.

You need both a model and coordinates to do a simulation.

Mark