[gmx-users] Problem with the autocorrelation of Rg

[faride badalkhani]

Kindly find the Rg plot in the following link:

https://www.dropbox.com/s/8yqkrr0hym6c899/Rg9-polymer%2BLigand.xlsx?dl=0

Let me know if you need any other files or information.

Regards,
F.

On Mon, Jan 23, 2017 at 2:07 PM, Erik Marklund <erik.marklund at kemi.uu.se>
wrote:

> Hi,
>
> Thanks. And the file Rg.xvg looks sound?
>
> Kind regards,
> Erik
>
> > On 23 Jan 2017, at 11:33, faride badalkhani <farideh.khamseh at gmail.com>
> wrote:
> >
> > Hi,
> >
> > Thanks for the answer. I used the autocorrelation function of the squared
> > radius of gyration cross-correlation of time course of Rg with itself
> with
> > the following command
> > gmx analyze -f Rg.xvg -ac
> >
> > and the autocorrelation is exactly zero.
> >
> > it is worth mentioning that I have performed the same PMF calculations
> on a
> > polymer-drug system and I did not have any problem in that case. The only
> > difference of that system with this one was in the terminal groups of
> > polymer. The first polymer has protonated surface groups (NH3+) but the
> > second one is neutral (acetylene).
> >
> > Best,
> > F.
> >
> > On Mon, Jan 23, 2017 at 1:42 PM, Erik Marklund <erik.marklund at kemi.uu.se
> >
> > wrote:
> >
> >> Dear Farideh,
> >>
> >> Can you please inform us about how you calculated the ac? Hard to help
> >> otherwise. Also, is it exactly zero or just very small numbers?
> >>
> >> Kind regards,
> >> Erik
> >>
> >>> On 23 Jan 2017, at 10:50, faride badalkhani <farideh.khamseh at gmail.com
> >
> >> wrote:
> >>>
> >>> Dear GROMACS users,
> >>>
> >>> I am performing umbrella sampling on a polymer-ligand system and I
> >> generate
> >>> configurations successfully but the problem is that when I plot the
> >>> autocorrelation function of Rg for each window it is zero for the whole
> >>> time of simulation. I changed the run time for each window but nothing
> >>> changed. Moreover, the initial polymer-ligand structure is equilibrated
> >>> well.
> >>> Any comment or suggestion will be greatly appreciated.
> >>>
> >>> Best,
> >>> Farideh
> >>> --
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