Hello David,
Thank you a lot for the answer. And yes it’s “three” and not “tree”, sorry for the repeated spelling mistake.
I’ll keep minimising the hole system then, I’m not aware of how small the GMAX and RMS values should be to consider that a system has been sufficiently minimised.
I watched both trajectories one from a QM/MM calculation and one from a MM calculation as you advised me to do, both molecular dynamics simulations starting from the same minimised structure.
In the QM/MM one, the bonds of the three water molecules become extremely long, as well as some other bonds (that I didn’t manage to identify yet..) leading to a blow up of the structure. The water molecules appear as triangles, as if there was a bond between the hydrogen atoms (!!).
In the trajectory from the MM calculation, one of the three water molecules slips away from the catalytic site and the rest of the system (protein+ligand+Mg ion+two other water molecules) remain quite stable. I’m surprised to see the water molecule diffuse away from the rest of the cluster as when comparing several minimised structures it seems that the assembly is stable and the positions of the water molecules don’t change significantly..
I’ll try to heat more slowly to see how the dynamics change. I will strongly appreciate any suggestion you may think could help me.
Thanks anyway,
Ruth
> On 15 Sep 2015, at 20:52, David A Case <david.case.rutgers.edu> wrote:
>
> On Tue, Sep 15, 2015, Ruth Helena Tichauer wrote:
>>
>> I’m running a molecular dynamics simulation of a protein with its
>> ligand and an Mg +2 ion in implicit solvent although there are tree
>> water molecules in the active region as they are necessary for the
>> reaction to proceed.
>
> I don't understand what you mean by the phrase "tree water molecule". (I
> first thought you meant to write "three", but this same phrase seems to
> persist in many emails....)
>
>>
>> The structure has been successfully quantum minimised (GMAX=40, RMS=1.8)
>> prior to the MD; treating only a few residues, the ligand, the Mg ion
>> and the water molecules quantum dynamically.
>
> This is not all that low an rms gradient; you might try more minimization.
>
>>
>> I tried to run the molecular dynamics simulation treating quantum
>> dynamically the same region of the system as during the minimisation but
>> got an error message saying “vlimit exceeded for step..”.
>
> I don't see anything obviously wrong with your input file, so details are
> probably critical here.
>
>
>>
>> I run then the same molecular dynamics simulation without the quantum
>> treatment. It was successfully achieved but one of the water molecules
>> had slipped away from the active site..
>> _How a water molecule could go so far away?
>
> We don't have enough information here: do you see anything that should prevent
> the water molecule from diffusing away from the rest of the cluster?
>
>> _Could the “special routines” of shake used for water molecules be
>> the reason of the “vlimit exceeded” when they are treated quantum
>> dynamically?
>
> This seems unlikely. Since you saved a trajectory file from the qm/mm
> calculation at every step, look at it closely in a program like VMD or Chimera
> to see if you can figure out what bad things are happening. Compare it to a
> similar trajectory without qm/mm.
>
> ...good luck...dac
>
>
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Received on Wed Sep 16 2015 - 06:30:04 PDT
