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