Asking for Free energy calculation advice

From: Kasra Fattah (
Date: Thu Dec 05 2013 - 14:18:20 CST

Hi All,

I'm doing a free energy calculation of a nano-particle with the reaction
coordinate being the center of the mass distance of the particle from a
wall with a water as solvent surrounding the particle and the wall. I
started the simulation with the particle far above the wall as it's
hydrophobic it soon find its way to land and stays on the wall. I'm doing
an ABF with colvars, after the particle reaches the wall it stays there for
a very long time, actually the simulation is still running and 8ns has
already passed but after the initial 2ns that took for the particle to
reach the wall it's spending rest of it on the wall.
Although the ABF is doing its job to negating the force on the particle (as
I checked it in the trajectory file of the colvars) but it how can I make
the particle to move around and sample the reaction coordinate? it's like
only the few bins near the wall are only sampled as the particle is stuck
there (maybe because it's waiting for the diffusion to kick it out of that
position?!) ...I would really appreciate it if you can comment on this kind
of situation and how I can circumvent this situation.


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