[gmx-users] Potential Energy-Umbrella sampling

[Mark Abraham]

Hi,

Your trajectory went from one thing to a completely different thing, so
what did your visual inspection of the trajectory tell you?

Mark

On Mon, 15 Jun 2015 17:54 gozde ergin <gozdeeergin at gmail.com> wrote:

> 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
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