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DMD Simulation Scale
09-27-2012, 08:12 AM
Post: #1
DMD Simulation Scale
Hello, I was just wondering if you knew approximately how piDMD scales with the system size. For example, with the most straight-forward MD, the scale is N^2 where N is the number of atoms in the system. I was wondering if I could find out how piDMD compares.

Thank you
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09-27-2012, 10:07 AM
Post: #2
RE: DMD Simulation Scale
Hi Jason,

DMD uses neighbor list opmization schemes, and in simple cases (e.g. gases) should scale linearly with N. This is similar to scaling of conventional MD that uses same optimization.
In case of proteins, scaling parameter can be larger than 1, as proteins often form compact structures.
Please, have a look at our recent publication (http://dx.doi.org/10.1021/jp2114576), where we have measured time required to simulate proteins of different lengths.

David
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