<br>Hi Bob,<br><br>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.
<br><br>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
<a href="http://md.chem.rug.nl/ndlp/">http://md.chem.rug.nl/ndlp/</a> 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
<a href="http://md.chem.rug.nl/~tsjerk/GMX/">http://md.chem.rug.nl/~tsjerk/GMX/</a> 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).<br>
<br>Hope it helps,<br><br>Tsjerk<br><br><br><div><span class="gmail_quote">On 11/30/05, <b class="gmail_sendername">Mark Abraham</b> <<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</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;">David Mobley wrote:<br>> Bob,<br>><br>> Lots of people have different opinions about this. My personal opinion is
<br>> that they should be more like the whole cutoff away from the box edge,<br>> although the answer probably depends on the properties you're trying to look<br>> at. One factor is that water properties are somewhat different near
<br>> proteins, etc. (i.e. there are solvation shells which extend out a ways<br>> before you really get to bulk water). So if an atom in one box can "feel"<br>> the altered water properties near the image of the protein in the next box,
<br>> it will give you slightly different answers.<br><br>The water properties will be more perturbed still if you have so little<br>solvation still that one water molecule feels the long-range influence<br>of multiple copies of the solute.
<br><br>Hunenberger and McCammon have a technique for assessing the extent to<br>which periodicity is perturbing the PMF of biomolecular systems - see J.<br>Chem. Phys. B. 104:3668 (2000) and related papers. In particular they
<br>opine that "For this specific system [polyalanine octapeptide with<br>charged termini], we would recommend the inclusion of at least three<br>solvation layers (about 0.85 nm) between the peptide termini and the<br>
nearest unit-cell walls. In fact, such a requirement is not<br>unrealistically drastic for the simulation of typical biomolecules."<br><br>> Again, it depends on what you're looking at. I'm doing free energy<br>> calculations where I disappear a ligand in a protein binding site (which is
<br>> buried) and it's sufficient for my purposes to use a box size which is only<br>> about 5A bigger in each direction than the largest protein dimension, even<br>> though my cutoffs are more like 9A. If there is a "conventional" wisdom on
<br>> this it is probably that you should use slightly larger box sizes than 5A<br>> extra in each direction, but for what I'm doing, it seems not to make a<br>> difference. This is already a fairly large system, too, so that probably
<br>> 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>Yes, it isn't the sort of question that untrained humans' judgement is
<br>any good at answering. It's a complex many-body through-space<br>interaction whose macroscopic effects may only be seen over long<br>simulation times (much longer than typical non-REMD simulations). You<br>need to look at your system, at *recent* literature, your computer
<br>hardware limitations and come up with something defensible.<br><br>Mark<br>_______________________________________________<br>gmx-users mailing list<br><a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
<a href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>Please don't post (un)subscribe requests to the list. Use the<br>www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">
gmx-users-request@gromacs.org</a>.<br></blockquote></div><br><br clear="all"><br>-- <br><br>Tsjerk A. Wassenaar, M.Sc.<br>Groningen Biomolecular Sciences and Biotechnology Institute (GBB)<br>Dept. of Biophysical Chemistry
<br>University of Groningen<br>Nijenborgh 4<br>9747AG Groningen, The Netherlands<br>+31 50 363 4336<br>