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