On Thu, Jan 27, 2011, Ashutosh Shandilya wrote:
> I am doing calculation for Fe -O complex where there is a free radical on
> one of the oxygen. After making the library file in and adding the required
> bond lengths, bond angle and dihedral parameter I was able to make the
> topology and coordinate file and did the minimization.
> So the question is can I do simulation with free radicals without changing
> anything in the force fields aka .gaff file.
Gaff doesn't know anything about iron, so whatever you get out will be what
you put in by hand. Molecular mechanics doesn't know about electrons, so does
not know or care whether the system is a free radical or not. But that means
that whatever assumptions you make in designing the force field will show up
in the results: if the input is "garbage", you know what to expect for the
output. But if you are interested in aspects of the simulation that do not
depend critically on how you describe the Fe-O group, you might be OK.
...dac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Jan 27 2011 - 06:00:03 PST
