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.
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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University of Florida Research Foundation Professor.
Department of Chemistry
University of Florida
roitberg.ufl.edu
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Received on Fri Sep 02 2016 - 11:00:05 PDT
