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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Received on Fri Sep 02 2016 - 11:00:03 PDT
