On Fri, Apr 28, 2017, Pengfei Li wrote:
>
> Recently, I want to calculate the solvation free energy of s small
> molecule fixed (rigid body) using pmemd TI simulations in AMBER.
Amber (as you already know) doesn't support rigid body dynamics.
> If I modify the code of pmemd by only setting the force and velocity of
> the fixed molecule zero, will the simulations have any other problems?
Yes: you are violating Newton's third law; the temperature won't be correct,
nor will the pressure. It might be that these (and other) problems would be
small, but it's hard to tell.
You could add "NMR" restraints to keep the solute approximately rigid; but
it's again hard to know how to evaluate the quality of the results. Maybe you
could find some thermodynamic cycles where it would make sense to assume
that the errors involved in "rigidifying" the molecule cancel.
....dac
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Received on Sun Apr 30 2017 - 17:30:03 PDT
