[gmx-users] Simulations with solvent shell

Mark Abraham Mark.Abraham at anu.edu.au
Tue Sep 22 23:18:24 CEST 2009

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).


> 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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