Dear all,
I am doing simulation with a polymer in TIP3P water now. The monomer has a 7membered ring. I used PARAMFIT to get a set of force field for it. I used TLEAP to combine monomers to a polymer and pack it with TIP3P water.
After running for 20ns (NPT), I extracted some fragment from the trajectory file. These fragments were all monomer with missing terminals. I added hydrogen atoms to makeup the terminals. And then I used Gaussian09 to do SP and OPT with MP2/6-31G* to see the potential difference.
The results showed the conformation extracted from MD simulation had much higher potential than its optimized conformation. I had 24 conformations. The biggest potential difference was 66kcal/mol. The smallest potential difference was 35kcal/mol.
I know AMBER could overcome small energy barrier, but the potential difference was too big. Is this condition normal?
Thanks,
Xiaoquan.
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Received on Mon Aug 17 2015 - 12:30:03 PDT
