> I am trying to do dynamics regarding solvation sugar molecules in ionic
> liquids. Could anyone help me how to create the ionic liquid solvent box
> using xleap? Ionic liquid that I will try to use is [Emim][TfO]
> (1-ethyl-3-methylimidazolium Trifluoromethylsulfonate).
>
> Ionic liquid is the liquid that is only composed of anion and cation. In
> case of [Emim][TfO], Emim(1-ethyl-3-methylimidazolium) is cation(+1),
> [TfO](Trifluoromethylsulfonate) is anion(-1).
You could make an initial box by solvating a single molecule in
layers:
> init = copy mol1
> solvatebox init mol2 4
> solvatebox init mol1 2
> saveamberparm init iobox.top iobox.crd
Then equilibrate the box with constant pressure, convert to pdb, and
> solbox = loadpdb solbox.pdb
> solvatebox mymol solbox 10
Or you could build up the layers directly around your solute, then put a
cartestian restraint on the solute while equilibrating it (as would
also be necessary if using an intermediate box to solvate the solute).
Likely it will be tricky to get 1:1 ionic ratio, but this will not matter
so much if you are making an ion-only box to then solvate another molecule,
since arbitrary adjustments will still be needed after solvating the other
molecule because of losing the ionic balance. The adjustments can be made
by editing the system in xleap and deleting extra solute molecules of the
appropriate species.
You might want to consider debugging your solvent molecules by first running
each separately with Na+ and Cl- to neutralize.
Bill
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Received on Mon May 03 2010 - 13:30:03 PDT
