Dear all,
I am trying to fix an atom of a polymer in my MD simulation to make a circumstance that the polymer is immoblized on some subtrate. At the beginning, I added a force constant 500kcal/mol to the atom, in tutorial B1, it said this was a very big number. But in my simulation, I found the atom moved around slowly. Should I increase the force constant? or is there any other method to fix one atom of a polymer in amber?
Additionally, is it possible to calculate free energy of some comformations in Amber?
Thanks,
Xiaoquan.
2013-11-23
X Sun
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Received on Sat Nov 23 2013 - 08:30:02 PST
