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
