Aditi Borkar wrote:
Dear Mark,
Thank you. I was indeed using pressure coupling.
My protein is crescent shaped so if I use a regular simulation box, I
get one with a large volume. I hoped that using a shell will reduce
the number of atoms in the system and will facilitate computation.
So should I just stick to the traditional way of using solvent boxes
to proceed with the simulations? Is there an alternative?
If you've got a well-formed solvent-shell protocol (e.g. no periodicity,
some kind of frozen and/or restrained layer of waters, some kind of
implicit electrostatic treatment outside the shell) then it's probably
about as reasonable to use that as anything else. Certainly with an
irregularly-shaped protein any kind of minimalist classic formulation of
solvent is risky... if your protein rotates with respect to the box then
you either need heaps of unnecessary solvent, or you'll have a serious
problem. Some kind of angle restraint to the Z axis might prove to be
the best approach (manual 4.3.2).
Mark
On Tue, Sep 22, 2009 at 6:45 PM, Mark Abraham <[email protected]> wrote:
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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