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 - 14:30:02 PDT
