I want to do molecular dynamics simulation of polymers. The polymer is composed of monomers and the monomers have different type of epimers. Is molecular dynamics able to reveal the difference between polymers consisting of different monomers? Or are they completely the same thing in the view of molecular dynamics?
For example, the monomer could be β-D-glucopyranose or β-D-mannopyranose. If the first molecule is built with solely β-D-glucopyranose, the second molecule is built with solely
β-D-mannopyranose, and the third molecule is built with a random combination of the two monomers. In molecular dynamics simulation, is the difference between the three molecules could be revealed?
The difference of β-D-glucopyranose and β-D-mannopyranose can be found at this Wikipedia link https://en.wikipedia.org/wiki/Epimer?oldformat=true
Any help would be much appreciated!
Mr. Liu,
Via ab initio or DFT MD, however. For instance, you could use Born-Oppenheimer MD.
Only spatial steric hindrance may cause selectivity. At this time, conventional MD can also give some explanations.
You can do a quick test to observe the proportion of various epimers in about 500 ns MD.
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