[gmx-users] adding a metal ion to the force field

[Jian Zou]

balamurugan r wrote:
> I have certain doubts with regard to adding a metal ion to the force 
> field.  Is it really enough
> 1.  to create a .itp file
> 2.  add the mass and charge details in the itp file
> 3.  and to add the name and mass of the metal ion in the atp file of the 
> force field.
>
> Will this suffice to define the metal ion in the frce field.

LJ parameter should also be added, if you introduce a new atom type.

And the name for the ion type should be chosen carefully, because eg. Na1 
has the meaning of the first atom in group Na, which will cause conflict.

If you only want to use a different charge for an existing ion, genion 
options -pq or -nq may help.


Regards,

Jian Zou