[gmx-users] Solvation box size

[Tsjerk Wassenaar]

Hi Bob,

Taking half the cut-off should in theory be enough to keep periodic images
from interacting, if you neglect effects due to water ordering. But you
should consider that your molecule moves and may undergo conformational
changes, which may definitely cause direct interactions. Though it's true
that there's no rule of thumb, I'd say you should at least take half the
cut-off and a bit more to allow movement. Frankly, I usually stick with a
distance to the wall of 1 nm (four layers of water) to be on the safe side
and to have a region of solvent inbetween periodic images which will display
more or less bulk-like behaviour.

If you're protein is not too flexible you may want to consider simulating it
in a tight-fitting box (Bekker et al. JCC 25: 1037 (2004)) which can cut the
system size down with 20-50% depending on the shape of your molecule. You
can submit your structure at http://md.chem.rug.nl/ndlp/ and mail me if
anything goes wrong. The simulation will have to be run with rotational
constraints for which you can take a modified gromacs version from
http://md.chem.rug.nl/~tsjerk/GMX/ We have recently shown that the usage of
such a box does not change the outcome of the simulations (Wassenaar and
Mark, JCC in press).

Hope it helps,

Tsjerk


On 11/30/05, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
>
> David Mobley wrote:
> > Bob,
> >
> > Lots of people have different opinions about this. My personal opinion
> is
> > that they should be more like the whole cutoff away from the box edge,
> > although the answer probably depends on the properties you're trying to
> look
> > at. One factor is that water properties are somewhat different near
> > proteins, etc. (i.e. there are solvation shells which extend out a ways
> > before you really get to  bulk water). So if an atom in one box can
> "feel"
> > the altered water properties near the image of the protein in the next
> box,
> > it will give you slightly different answers.
>
> The water properties will be more perturbed still if you have so little
> solvation still that one water molecule feels the long-range influence
> of multiple copies of the solute.
>
> Hunenberger and McCammon have a technique for assessing the extent to
> which periodicity is perturbing the PMF of biomolecular systems - see J.
> Chem. Phys. B. 104:3668 (2000) and related papers. In particular they
> opine that "For this specific system [polyalanine octapeptide with
> charged termini], we would recommend the inclusion of at least three
> solvation layers (about 0.85 nm) between the peptide termini and the
> nearest unit-cell walls. In fact, such a requirement is not
> unrealistically drastic for the simulation of typical biomolecules."
>
> > Again, it depends on what you're looking at. I'm doing free energy
> > calculations where I disappear a ligand in a protein binding site (which
> is
> > buried) and it's sufficient for my purposes to use a box size which is
> only
> > about 5A bigger in each direction than the largest protein dimension,
> even
> > though my cutoffs are more like 9A. If there is a "conventional" wisdom
> on
> > this it is probably that you should use slightly larger box sizes than
> 5A
> > extra in each direction, but for what I'm doing, it seems not to make a
> > difference. This is already a fairly large system, too, so that probably
> > helps. I'm being more careful when it comes to small molecules.
> >
> > Sorry I can't be more definitive. And other people may disagree with me.
>
> Yes, it isn't the sort of question that untrained humans' judgement is
> any good at answering. It's a complex many-body through-space
> interaction whose macroscopic effects may only be seen over long
> simulation times (much longer than typical non-REMD simulations). You
> need to look at your system, at *recent* literature, your computer
> hardware limitations and come up with something defensible.
>
> Mark
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--

Tsjerk A. Wassenaar, M.Sc.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747AG Groningen, The Netherlands
+31 50 363 4336
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