[gmx-users] Simulations with solvent shell

Aditi Borkar aditi.borkar at gmail.com
Tue Sep 22 15:39:44 CEST 2009

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?

Thank you.

On Tue, Sep 22, 2009 at 6:45 PM, Mark Abraham <Mark.Abraham at anu.edu.au> 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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Aditi Borkar,
Tata Institute of Fundamental Research,

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