Sorry about this follow up. But I guess that if I don't set the fcap
variable in the mdin file, the restraints won't work, right?
But I still would appreciate if you could answer my second question. What
is the syntax for a list in the solvatecap command?
Thank you
Fabrício
2016-08-09 11:07 GMT-03:00 Fabrício Bracht <fabracht1.gmail.com>:
> Hello. Does the solvateshell command in tleap work for what we've
> discussed? I mean does it create a cap around the solute with the
> restraining half-harmonic potential in the prmtop file? I have tried to
> simulate a 'water drop' created by solvateshell and the simulation, but
> there is one water molecule that has escaped. At least that is what I see
> when I calculate the distance with cpptraj.
> If I am actually supposer to use solvatecap from tleap, how do I pass a
> list of residues to solvatecap? I have tried:
> solvatecap mol TIP3PBOX mol.1 mol.244 12. 0.8
> solvatecap mol TIP3PBOX mol.1-mol.244 12. 0.8
> solvatecap mol TIP3PBOX mol.[1-244] 12. 0.8
> solvatecap mol TIP3PBOX mol.{1-244} 12. 0.8
> None of these work.
> Thank you
> Fabrício
>
> 2016-08-06 17:18 GMT-03:00 Dr. Andreas W. Goetz <agoetz.sdsc.edu>:
>
>> Thanks Fabricio, this is a useful reference, captures the points that we
>> discussed.
>>
>> 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 6:30 PM, Fabrício Bracht <fabracht1.gmail.com>
>> wrote:
>> >
>> > 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 Tue Aug 09 2016 - 07:30:02 PDT
