[gmx-users] Problem with the autocorrelation of Rg

[faride badalkhani]

Dear Erik,

I could reproduce the desired results using xmgrace as you said. I really
appreciate your help. And I have one more question. For one of
polymer-ligand the PMF profile goes down at long distances, while the
histogram windows are distributed evenly. The US run time is 5 ns. Could
you help me on this issue?
You can find the profile in the following link:

https://www.dropbox.com/s/8k1e0eqm80osg7j/profileNH2.xlsx?dl=0

Regards,
Farideh



On Mon, Jan 23, 2017 at 11:47 PM, faride badalkhani <
farideh.khamseh at gmail.com> wrote:

> Dear Erik,
>
> Thank you so much for the time and answer. Actually, I just tried the gmx
> command to get autocorrelation. I did not know that xmgrace can perform
> that. I will try to get ACF with xmgrace and then compare the results.
>
> Regards,
> Farideh
>
> On Mon, Jan 23, 2017 at 6:55 PM, Erik Marklund <erik.marklund at kemi.uu.se>
> wrote:
>
>> I can reproduce your result, and if I change the value of a single
>> datapoint by, say 5% or so, I get a non-zero acf. It could be that cmx
>> analyze is too insensitive for numeric reasons, or it could also be that
>> your data is too sparsely sampled to contain any trace of “memory” in the
>> system. Have you tried calculating the act by other means, xmgrace for
>> instance? Does that yield a similar result?
>>
>> Kind regards,
>> Erik
>>
>> > On 23 Jan 2017, at 12:08, faride badalkhani <farideh.khamseh at gmail.com>
>> wrote:
>> >
>> > Kindly find the Rg plot in the following link:
>> >
>> > https://www.dropbox.com/s/8yqkrr0hym6c899/Rg9-polymer%2BLiga
>> nd.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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