[gmx-users] Potential Energy-Umbrella sampling

[gozde ergin]

Hi all,

My system has 560 water molecules covered by  50 organic molecules. I run
the simulation for 20 ns and here is my potential energy figure.

http://imgur.com/l9mJesD,ggDDZtb#0 (first pic)


I just could not understand what is going on after 7.5 ns?

Also I am doing this simulation to calculate the PMF. On the links there
are two PMF curves for the same system for 4ns and 20ns. They are pretty
different! (4 ns seems more realistic)

http://imgur.com/l9mJesD,ggDDZtb#0 (second pic).

What could be the reason to get two very different PMF curve for the same
system?

bests