Bob,<br>
<br>
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. <br>
<br>
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.<br>
<br>
Sorry I can't be more definitive. And other people may disagree with me.<br>
<br>
David<br>
<br><br><div><span class="gmail_quote">On 11/29/05, <b class="gmail_sendername">Bob Johnson</b> <<a href="mailto:robertjo@physics.upenn.edu">robertjo@physics.upenn.edu</a>> wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hello everyone,<br>What is a good rule of thumb for creating solvation boxes and using periodic<br>boundary conditions? For example, I am currently positioning molecules in a box<br>so that they are about 1/2 of the LJ cutoff away from the box edge. This is to
<br>ensure that each molecule doesn't interact with its image. Is this a good<br>method?<br>Thanks,<br>Bob Johnson<br>_______________________________________________<br>gmx-users mailing list<br><a href="mailto:gmx-users@gromacs.org">
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