I know. Sorry, I should have sent you the updated example.
In the case of a solvent cap, since one cannot use implicit solvation with
QM/MMext simulations, does this mean that the rest of the protein will
effectively be in a vacuum? And if so would it be wise to apply some
restraining force on the atoms. There are some very mobile groups in my
structure. Would this be better than using cutoff with a periodic
simulation in NVT (since the cutoff in NVE leads to discotinuities)?
Thank you
Fabrício
2016-08-05 10:50 GMT-03:00 David A Case <david.case.rutgers.edu>:
> On Thu, Aug 04, 2016, Fabrício Bracht wrote:
>
> > Thank you David. But, for the qm/mm md simulation, by specifying ntb=0
> > would mean I would not be using periodic conditions, right?
>
> Correct: but in your example input, you did not specify ntb=0, and you
> clearly
> had a periodic simulation. (Defualt is ntb=1).
>
> ...dac
>
>
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Received on Fri Aug 05 2016 - 11:30:03 PDT
