[gmx-users] Solvation box size

David Mobley dmobley at gmail.com
Tue Nov 29 18:38:43 CET 2005


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.

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.


On 11/29/05, Bob Johnson <robertjo at physics.upenn.edu> wrote:
> Hello everyone,
> What is a good rule of thumb for creating solvation boxes and using
> periodic
> boundary conditions? For example, I am currently positioning molecules in
> a box
> so that they are about 1/2 of the LJ cutoff away from the box edge. This
> is to
> ensure that each molecule doesn't interact with its image. Is this a good
> method?
> Thanks,
> Bob Johnson
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