On 2 September 2016 at 18:59, Adrian Roitberg <roitberg.ufl.edu> wrote:
>
>
> On 9/2/16 11:57 AM, Fabrício Bracht wrote:
> > Yes, all qm/mm studies should be published here
> > http://www.newdawnmagazine.com/tag/occult.
> > Thanks for the flat restraint tip. You mean something like this: (I
> suppose)
> > &rst iat=3218,3220, r1=-30, r2=1.9, r3=3.0, r4=30.0, rk2 = 160., rk3 =
> > 160., rstwt=1.0, /
> correct, that will keep the distance between atoms 3218 and 3220 between
> 1.9 and 3.0 A with no energy cost, but it will bring that distance back
> to earth if it ever goes above.
>
> For bonds that break (but shouldn't!), I usually use a one-sided
harmonic(-like) restraint, by setting rk2=0.
Marc
> adrian
>
> >
> > Fabrício
> >
> > 2016-09-02 14:54 GMT-03:00 Adrian Roitberg <roitberg.ufl.edu>:
> >
> >> Welcome to the part of QM/MM that resembles black magic !
> >>
> >> We have seen things like that
> >>
> >> A possible solution, if you REALLY know your reaction and are willing to
> >> intervene, is to put a very soft, flat restraint, in the bonds that are
> >> going bad but you know they should stay put. I presume you understand
> >> what I mean by flat restraint. Just add it to the nmropt data in a way
> >> that does not allow the atoms to become too close or to far away.
> >>
> >> Adrian
> >>
> >>
> >>
> >> On 9/2/16 11:46 AM, Fabrício Bracht wrote:
> >>> Hmmm. Glad to hear that. It makes life a bit easier. Now, I posted a
> >>> question yesterday on the list asking about the use of shake on qm
> >> regions.
> >>> I understand that it might seem like a very naive question, but it
> >>> something to do with what we are talking now. Would it be wrong to
> assume
> >>> that the only atoms that need not to be shaken are the ones involved
> >>> directly in the reaction? I know that once you specify the qm atoms and
> >>> state qmshake = 0 you cannot use shake on any of those atoms. The
> >>> noshakemask has to list all the atoms in the qm region, right? But,
> what
> >>> would happen if you applied restraints to all the atoms that are not
> >>> directly involved in the reaction.
> >>> I ask this, because I have noticed that, sometimes, a hydrogen from a
> >>> carbon that is adjacent to the group participating in the reaction (for
> >>> example, HB2 linked to CB2 next to the reacting carboxylate of a
> >> aspartate
> >>> residue) is the one that explodes first.
> >>>
> >>> Fabrício
> >>>
> >>> 2016-09-02 14:37 GMT-03:00 Adrian Roitberg <roitberg.ufl.edu>:
> >>>
> >>>> Hi Fabricio.
> >>>>
> >>>> Indeed, we have found the same. By the way, this is common in any type
> >>>> of QM/MM calculations, not just umbrella. QM is very finicky and can
> >>>> blow up when some coordinates are just a little bit off.
> >>>>
> >>>> However, when we encounter the issues you found, we do not go all out
> >>>> and minimize + change T slowly. Usually, a VERY small number of
> >>>> minimization steps is enough, since the problem is mostly localized
> in a
> >>>> single bad contact.
> >>>>
> >>>> Adrian
> >>>>
> >>>>
> >>>>
> >>>> On 9/2/16 11:34 AM, Fabrício Bracht wrote:
> >>>>> Indeed it is. But I have been doing some testings, and was about to
> ask
> >>>>> this in the list myself. When doing reaction paths with umbrella
> >>>> sampling,
> >>>>> I have found that the coordinates with high energy values on the
> >> reaction
> >>>>> path have a really (really really) high tendency on exploding. I
> tried
> >>>>> loads of different starting configurations and found that, in most
> >> cases,
> >>>>> adding a previous minimization, with the umbrella restraints on,
> solved
> >>>>> this problem. I did this in two different ways. The first was adding
> a
> >>>>> nmropt coupling to slowly increase the temperature, and the second I
> >> only
> >>>>> set the temperature to the final value I wanted and started the
> >>>> simulation
> >>>>> anyways. See that in both cases the simulation time for the QM/MM
> >>>> umbrella
> >>>>> window had to be increased to accommodate the thermalization. I
> didn't
> >>>>> expect that the simulation with no slow thermalization to finish,
> but,
> >>>> for
> >>>>> my surprise, those were the ones that worked without any errors. By
> my
> >>>>> calculations, I lost less time doing this minimization procedure and
> >>>>> increasing the simulation time than repeatedly restarting crashed
> >>>>> simulations.
> >>>>> I did this for a reaction I had already calculated the PMF and the
> >>>> results
> >>>>> were very, very similar. The reaction barrier increased by 0.2
> kcal/mol
> >>>> and
> >>>>> the deltaPMF(final-initial) increased by 0.2.
> >>>>> I did this by sheer curiosity, as I had already done this simulation
> >> and
> >>>> I
> >>>>> knew the system quite well. But I found the results quite
> interesting.
> >>>>> What do you guys think?
> >>>>>
> >>>>> Fabrício
> >>>>>
> >>>>> 2016-09-02 14:09 GMT-03:00 Adrian Roitberg <roitberg.ufl.edu>:
> >>>>>
> >>>>>> no, there is not, but this is not a small issue !
> >>>>>>
> >>>>>> But, if you eventually want to run QM/MM MD, as Gustavo said, you
> will
> >>>>>> have to reheat, re-relax the system at the QM/MM level, which is
> much
> >>>>>> more expensive than the MM one.
> >>>>>>
> >>>>>> adrian
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>> On 9/2/16 11:03 AM, Fabrício Bracht wrote:
> >>>>>>> Is there a reason, other than loosing previous velocity
> information,
> >>>> for
> >>>>>>> *not* minimizing the structures?
> >>>>>>>
> >>>>>>>
> >>>>>>> 2016-09-02 13:17 GMT-03:00 Gustavo Seabra <
> gustavo.seabra.gmail.com
> >>> :
> >>>>>>>> Hi Anna,
> >>>>>>>>
> >>>>>>>>> I have already carried out a classical molecular dynamic of my
> >>>> system.
> >>>>>>>> Continuously, I want to perform a QM/MM minimization starting from
> >> one
> >>>>>>>> snapshot of the MD. How can I do it?
> >>>>>>>>
> >>>>>>>> In principle, if you have already run a classical MD on the
> system,
> >>>> all
> >>>>>>>> you have to do is tweak the mdin file with the new keywords for
> >> QM/MM
> >>>>>> and
> >>>>>>>> minimization, then using the restart file from the MD simulation
> as
> >>>>>> input
> >>>>>>>> structure. Very much as if you were just continuing a classical MD
> >>>>>>>> calculation. (Of course, take care of the points raised earlier by
> >>>>>> Adrian
> >>>>>>>> and Andreas.)
> >>>>>>>>
> >>>>>>>> However, if your goal is to run a QM/MM MD, IMHO you should *not*
> >>>>>> minimize
> >>>>>>>> the geometry all over again. Just turn on the QM hamiltonian and
> run
> >>>>>> for a
> >>>>>>>> while to adjust the system to the new hamiltonian, keeping the
> same
> >>>>>>>> ensemble variables as before. (You may nee to adjust dt for a
> >> smaller
> >>>>>> step
> >>>>>>>> size.)
> >>>>>>>>
> >>>>>>>> —
> >>>>>>>> Gustavo.
> >>>>>>>>
> >>>>>>>>
> >>>>>>>> _______________________________________________
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> >>>>>>> _______________________________________________
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> >>>>>> --
> >>>>>> Dr. Adrian E. Roitberg
> >>>>>> University of Florida Research Foundation Professor.
> >>>>>> Department of Chemistry
> >>>>>> University of Florida
> >>>>>> roitberg.ufl.edu
> >>>>>> 352-392-6972
> >>>>>>
> >>>>>>
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> >>>> --
> >>>> Dr. Adrian E. Roitberg
> >>>> University of Florida Research Foundation Professor.
> >>>> Department of Chemistry
> >>>> University of Florida
> >>>> roitberg.ufl.edu
> >>>> 352-392-6972
> >>>>
> >>>>
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> >> --
> >> Dr. Adrian E. Roitberg
> >> University of Florida Research Foundation Professor.
> >> Department of Chemistry
> >> University of Florida
> >> roitberg.ufl.edu
> >> 352-392-6972
> >>
> >>
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> --
> Dr. Adrian E. Roitberg
> University of Florida Research Foundation Professor.
> Department of Chemistry
> University of Florida
> roitberg.ufl.edu
> 352-392-6972
>
>
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Received on Fri Sep 02 2016 - 12:30:02 PDT
