On Tue, Dec 06, 2016, A kS wrote:
>
> I am new to the MD simulation package AMBER. I have a
> protein-polynulceotide complex. I want to run a simulation in NPT, explicit
> solvent PBC condition where I can selectively switch of the interaction
> between protein and the polynucleotide. Is it at all possible??
No. You should think carefully about what you really want to do, and why.
If you switch off the interaction, then atoms of the protein can be in the
same place at atoms from the polynucleotide, which would not make any physical
sense.
More generally, because of the way PME works, energies in these simulations
are not "pairwise decomposible": this means that the total energy is not
simply the sum of pairwise terms, and that you cannot (easily) turn some terms
"on" and "off".
....dac
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Received on Tue Dec 06 2016 - 05:00:03 PST
