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.
Why did you define a spherical shell inside a periodic box? This will
get the worst of all worlds - periodicity artefacts, finite-size effects
and boundary effects.
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.
That's normal.
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)
The box will only change size if you are using pressure-coupling, but
you've not told us about this.
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.
The whole box can't shift... it's periodic, and there's no preferred
unit cell. If you'd prefer a particular arrangement of box and atoms
then you need to read trjconv -h, consider the various options and
experiment until you're happy.
Please let me know whether these observations are acceptably normal.
It seems very unlikely that you have both the simulation you hoped you'd
have and a successful simulation :-)
Mark
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