Hello Jason,
Thank you for the explanations.
It’s absolutely right that water exchanges readily but as I was running the calculation in implicit solvent, I thought that the water molecule in the active site couldn’t be replaced by another, ergo I wouldn’t be able to get the information I’m looking for.
Does the “variable solvent “ QM/MM approach works in implicit solvent?
I started running the minimisation+molecular dynamics simulation in explicit solvent to compare.
Thanks a lot for your help,
Ruth
> On 16 Sep 2015, at 17:07, Jason Swails <jason.swails.gmail.com> wrote:
>
> On Wed, Sep 16, 2015 at 9:16 AM, Ruth Helena Tichauer <rhtichau.laas.fr>
> wrote:
>
>> 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 (!!).
>>
>
> There *is*, if you're using one of the TIPnP water models. It's a rigid
> water model, so the 3 bonds correspond to the 3 constrained distances.
>
> However, all MM bonds are removed from the QM region, so this is not a
> cause for concern (the bonds still exist in the prmtop file, which is why
> VMD draws them).
>
>
>
>>
>> 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..
>>
>
> Why? Water exchanges readily in most processes like this (simple entropy,
> after all)... Keep in mind that minimization and MD are different -- the
> former simply reduces to a local minimum, whereas the latter allows
> particles to move.
>
> The "variable solvent" QM/MM approach was designed to deal with solvent
> exchanging by updating the "QM" waters as they exchange with MM waters.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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Received on Fri Sep 18 2015 - 02:00:04 PDT
