[gmx-users] Simulations with solvent shell

[Justin A. Lemkul]

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

-Justin

> Please let me know whether these observations are acceptably normal.
> 
> Thank you
> Aditi Borkar,
> Tata Institute of Fundamental Research,
> Mumbai.
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-- 
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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
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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