[gmx-users] Problem with the autocorrelation of Rg

[Erik Marklund]

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
>>> --
>>> Gromacs Users mailing list
>>> 
>>> * Please search the archive at http://www.gromacs.org/
>> Support/Mailing_Lists/GMX-Users_List before posting!
>>> 
>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>> 
>>> * For (un)subscribe requests visit
>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-request at gromacs.org.
>> 
>> --
>> Gromacs Users mailing list
>> 
>> * Please search the archive at http://www.gromacs.org/
>> Support/Mailing_Lists/GMX-Users_List before posting!
>> 
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> 
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-request at gromacs.org.
>> 
> -- 
> Gromacs Users mailing list
> 
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
> 
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> 
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.