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 Tue Sep 15 2015 - 12:00:10 PDT
