[gmx-users] Simulations with solvent shell

Justin A. Lemkul jalemkul at vt.edu
Tue Sep 22 15:07:56 CEST 2009

Aditi Borkar wrote:
> Dear All,
> I created a simulation box in editconf with -d 2.5. Then in genbox, I
> used the -shell 1.4 option to define a 1.4 nm thick layer of solvent
> around my protein. When I visualized the system in Rasmol, as
> expected, there was a lot of "empty space" in the simulation box.
> Should this vacuum create any artifacts in PBC or other energy
> calculations? I did not receive any warnings or messages and so
> continued with the MD simulation.

Well, you didn't receive any warnings, because as far as Gromacs is concerned, 
you are doing something that is possible :)

Is your goal to simulate a protein in a droplet surrounded by vacuum?

> During the MD, I saw that some ( <10) water molecules travel away from
> the shell/layer around the protein and come to lie in the vacuum of
> the box. Correspondingly the box size also varies depending upon the
> presence of such water molecules. After about 60 ps, the box reduced
> in size to just accommodate the solvent shell around the protein. And
> as yet the solvent forms a layer around the protein and is not
> distributed evenly in the box. By 100 ps the solvent molecules no more
> form a layer but are distributed evenly within the box (cube)

I'm assuming you are using pressure coupling, so the box will deform to 
accommodate the shape and size of your system.  Perhaps NVT might be a more 
suitable ensemble?

> One last observation is that when I viewed this trajectory in VMD, the
> molecule seemed to translate in space. There's no option to view the
> unitcell in VMD, so I do not know whether the whole box is shifting or
> just the protein+solvent is shifting inside the box.

Yes there is.  Use the Tk console:

package require pbctools
pbc box


> Please let me know whether these observations are acceptably normal.
> Thank you
> Aditi Borkar,
> Tata Institute of Fundamental Research,
> Mumbai.
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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