Hello everybody,
I've been working with a system where it would be exceedingly useful to put
a 10-12 potential between iron and any solvent oxygen to better simulate
water's behavior in the cavity. The parameters I am using for heme produce
excellent geometries and I'd like to leave them intact.
This leads me to ask you all:
1 - Do 10-12 potentials, via HBOND, still work in Amber14, and are they
supported in the CUDA implementation?
2 - The syntax from the frcmod file specification simply says atom types,
does this indicate that the 10-12 potential can be defined for any atom
type pairs?
3 - Does anyone know the function for this potential? I read that it had
coefficients of 5 and 6 on the 10th and 12th power terms respectively, but
I just wanted to confirm.
3 - Is there some major consideration that I am overlooking that will ruin
my results or otherwise break pmemd?
Thanks,
-David Poole
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Received on Fri Mar 13 2015 - 21:00:02 PDT
