[gmx-users] Force field parameters in water or in vacuum?

[Mark Abraham]

Chih-Ying Lin wrote:
> Hi
> For one molecule, will Gromacs give the same set of force field
> parameters to this molecule no matter this molecule is put in water or
> in vacuum?
> The bond length, the bond angle, and the dihedral angles of the same
> molecule will be different in water and in vacuum.
> So, will the force field parameters be changed/ adjusted in water than
> in vacuum?

Assignment of force field parameters happens (e.g. by hand or with 
pdb2gmx) before it is possible to verify whether a solvent or vacuum 
simulation is intended. So you could do whatever you want and GROMACS 
isn't going to change things on you or prevent you from doing things... 
but probably most of these things aren't sensible. See 
http://wiki.gromacs.org/index.php/Force_Fields

You should pick a force field that is known to work for the kind of 
calculation you want to do.

> How does Gromacs set the force field parameters for the molecule?

In pdb2gmx, atoms in residues have their names matched to a database of 
residues (.rtp files), which then looks up the interactions in yet 
another database (.atp and .itp files).

> I mean..... are the force field paramters determined in local or in global?

I don't know what you mean.

> Could I change parts of  the force field parameters which I found from
> the published paper?

Yes, but this would be a very bad idea for someone starting their MD 
experience. See http://wiki.gromacs.org/index.php/Parameterization

> Or, I could not change parts of the force field parameters; instead, I
> have to change the whole set of the force field
> parameters???

Read carefully and choose something appropriate in advance, so that 
"changing" doesn't arise.

Mark