[gmx-users] Potential Energy-Umbrella sampling

[gozde ergin]

I am using md-vv as an integrator but if I use m , I don't see this drift
(movement) in my system.
This is also another problem that I could not figure out.

On Mon, Jun 15, 2015 at 6:04 PM, gozde ergin <gozdeeergin at gmail.com> wrote:

> 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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