Hi all,
I have two questions about PMF calculations.
1) Which one is more suggested for an AFM pull simulation, an NVT or an NPT
ensemble? I am trying both vacuo and solvated runs (with OPLS-AA ff).
2) My second question is about solvation: I found out that pulling action is
much smoother in solvent than in vacuo. It may be bad to have energy and rms
jumps in vacuo. On the other hand, I think it would be
better for estimating forces and energy differences with an abrupt
change in the system. What is you opinion about effects of solvation?
Thanks in advance
Murat Cetinkaya
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