[gmx-users] Simulations with solvent shell

Aditi Borkar aditi.borkar at gmail.com
Tue Sep 22 15:02:35 CEST 2009

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.

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)

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.

Please let me know whether these observations are acceptably normal.

Thank you
Aditi Borkar,
Tata Institute of Fundamental Research,

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