You can switch off periodic boundary conditions by setting ntb=0, but it does not seem like a good idea for a simulation that has been set up for periodic boundary conditions (water box). Iff you want to avoid periodic boundary conditions, you should use a solvent cap. This can be done with the solvatecap command in leap, which also adds the restraining half-harmonic potential to the prmtop file. It is also possible to cut a solvent cap from a larger water box by setting ivcap=1 in the cntrl namelist (section 18.6.10 in the Amber 16 manual), but I have never done this and don’t know how well this works.
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 4, 2016, at 7:04 PM, Fabrício Bracht <fabracht1.gmail.com> 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? In this case,
> does the iwrap in the input file takes care of arranging things neatly
> inside the box or do I need to get a starting .rstrt file pre imaged with
> cpptraj?
> Thank you
> Fabrício
>
> 2016-08-04 18:38 GMT-03:00 David A Case <david.case.rutgers.edu>:
>
>> On Thu, Aug 04, 2016, Fabrício Bracht wrote:
>>> Sorry for not waiting a response, but I have tested with a minimization
>> and
>>> got the following problem:
>>
>>> cut=9999.0,
>>
>> You could do this in a non-periodic system, but not in a periodic one.
>> The cutoff needs to be less than half the smallest box dimension.
>>
>>> qmcut=9999.0
>>
>> Similar restrictions on qmcut, I think.
>>
>>> |Largest sphere to fit in unit cell has radius = 33.962
>>
>> Cutoffs must be less than this radius (minus some correction for the
>> "skin",
>> usually 2 Ang.)
>>
>> ....dac
>>
>>
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Received on Thu Aug 04 2016 - 23:30:02 PDT
