[gmx-users] Potential Energy-Umbrella sampling

[gozde ergin]

Hi Mark,

What do you mean by saying "thing"? Is phase changing?

I visualized in VMD but could not manage to really captured the difference
before 7.5 ns and after 7.5 ns.
Also because during the simulation all bulk is moving in the box but
distances between pullgroups stays constant so it is not easy to capture
what is going on there.

On Mon, Jun 15, 2015 at 5:58 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> 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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