[gmx-users] Re: Small V.S. Large simulation box.
leafyoung81-group at yahoo.com
Thu Mar 9 11:00:16 CET 2006
My conclusion with PME on small box comes from experience. As you are
comparing the results with experiments, you may would like to try
cut-off (set according to the force field you are using)/reaction
field/ewald sum beside PME?
> Dear Dr. Mark and Yang:
> Thanks for your quick response and suggestions.
> The box I used is a rhombic box, which is obtained based on hexgonal prism with "editconf -angles 90 90 120",
> and the size for this box is 2.8x2.8x4nm^3. The cutoffs are respectively rlist=rcoulomb=0.9nm, rvdw=1.2nm.
> Maybe, grid size significantly affect my results, I am trying now. Actually, I also do not want to use such
> a box, but it is from experimental equipments. So, I have to try. As a fact, there are almost no solvation shell
> between some of solute surfuce and box edge, which is possibly the reason for the unsatisfield results. But how to
> deal with it? I have to beg your help.
> Thanks again.
> Xie Yinghong
> > Yang Ye wrote:
> >>/ As being iterated for many times in this list, use of PME shall be only
> />>/ applicable to box of certain size, not too small. The default grid size
> />>/ for PME is 0.095, with a 0.2nm box, there is only two points. And I
> />>/ don't think this can be lifted simply by further decreasing grid size.
> > I haven't heard of any practical minimum box size necessary for
> > effective application of PME. I couldn't find mention of it on a quick
> > search of the gmx-users list. Can you provide a pointer, please? I can't
> > see any reason for such a minimum from the theory.
> > You can actually set the grid spacing for Ewald methods to anything
> > within reason. The default value of the fourierspacing parameter is
> > 0.12nm - which is a maximum grid spacing. Yinghong's solvation shell was
> > width around 0.2nm, not the box length, which he didn't tell us.
> > Mark
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