[gmx-users] Problem with the autocorrelation of Rg

[faride badalkhani]

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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