[gmx-users] Re: Small V.S. Large simulation box.

Yinghong xieyh at hkusua.hku.hk
Fri Mar 10 02:28:46 CET 2006

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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