[gmx-users] Thank you

[Mark Abraham]

Sunil Thapa wrote:
> Respectable Mark
> Thank you very much for your immediate response.
> I have added new atom type in the ffgmx.atp file and also modified 
> ffgmx.itp, ffgmxnb.itp. After that the pdb2gmx worked. I used genbox to 
> add water in the oxygen molecule system. For now I have taken only 2 
> oxygen molecules with the box size 1 nm.
> I have run the energy minimization. The potential energy came to be 
> -1.632 KJ/mole.

ffgmx is *deprecated*. That means you should not be using it for new 
simulations. Read the literature to try to find a suitable force field.

> Can I be hopeful that I will be able to go to production job, and Most 
> important thing is I need value of O-O bond constant for harmonic 
> potential. Could you provide me with that.

No. This is a highly non-trivial question. See 
http://wiki.gromacs.org/index.php/Parameterization

Mark