That is a good point. Found this while searching on the subject. Maybe
you've seen it already.
http://pubs.acs.org/doi/abs/10.1021/acs.jctc.6b00269?journalCode=jctcce
2016-08-05 18:17 GMT-03:00 Dr. Andreas W. Goetz <agoetz.sdsc.edu>:
> The solvent cap should be large enough to solvate the entire protein and
> keep it solvated during the simulation, such that only water will be at the
> vacuum boundary. The question is whether you prefer to simulate a protein
> in a highly concentrated solution or in a tiny water droplet. I am not
> generally advising against using PBC with a large qmcut value for NVT
> simulations, which is common practice. But you should be aware that there
> are discontinuities in the potential energy surface. The error due to the
> use of approximate force fields and QM Hamiltonians is most likely larger.
>
> All the best,
> Andy
>
> —
> Dr. Andreas W. Goetz
> Assistant Project Scientist
> San Diego Supercomputer Center
> Tel: +1-858-822-4771
> Email: agoetz.sdsc.edu
> Web: www.awgoetz.de
>
> > On Aug 5, 2016, at 11:06 AM, Fabrício Bracht <fabracht1.gmail.com>
> wrote:
> >
> > 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 - 19:00:02 PDT
