[gmx-users] PMF of a single water molecule respect to a surface

Alexander Alexander alexanderwien2k at gmail.com
Fri Feb 12 14:48:26 CET 2016

Dear Gromacs user,

I am calculation the PMF of a single water molecule to pull it away from
top of metallic surface along vacuum in the Z direction ,following the
Justin umbrella tutorial. I am only  interested in the behavior of PMF in
0.002 nm to 0.8 nm intervalon top of the surface, but I do not why the
population of the generated frames in this interval is really low and then
the result is so poor.

So, would you please let me know which parameter I should play around with?

I just tried 0.001 instead 0.01 as the "pull_coord1_rate" and simultaneously
3500 instead of 1000 as "pull_coord1_k", but the result got even worse.

Best regards,


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