[gmx-users] AFM pull and ensembles
muc176 at psu.edu
Mon Sep 4 20:20:11 CEST 2006
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
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