[gmx-users] Problem with the autocorrelation of Rg

[Erik Marklund]

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%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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