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
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