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, /
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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> >>>> --
> >>>> 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 - 11:00:05 PDT
