Re: [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.kham...@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 
> 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 
>> 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.markl...@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.kham...@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.markl...@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.kham...@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-requ...@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
>> 
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>>  https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
>> or
>>  send a mail to gmx-users-requ...@gromacs.org.
>> 
>> >>> --
>> >>> Gromacs Users mailing list
>> >>>
>> >>> * Please search the archive at http://www.gromacs.org/
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>> >>>
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>> >>> 

Re: [gmx-users] Problem with the autocorrelation of Rg

[faride badalkhani]

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 
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 
> 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  >
> > wrote:
> >
> >> Hi,
> >>
> >> Thanks. And the file Rg.xvg looks sound?
> >>
> >> Kind regards,
> >> Erik
> >>
> >>> On 23 Jan 2017, at 11:33, faride badalkhani  >
> >> 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.markl...@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.kham...@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-requ...@gromacs.org.
> 
>  --
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> 
>  * Please search the archive at http://www.gromacs.org/
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> 
> >>> --
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Re: [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  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 
> wrote:
> 
>> Hi,
>> 
>> Thanks. And the file Rg.xvg looks sound?
>> 
>> Kind regards,
>> Erik
>> 
>>> On 23 Jan 2017, at 11:33, faride badalkhani 
>> 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 >> 
>>> 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 >> 
 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-requ...@gromacs.org.
 
 --
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 * 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-requ...@gromacs.org.
 
>>> --
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>> send a mail to gmx-users-requ...@gromacs.org.
>> 
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Re: [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 
wrote:

> Hi,
>
> Thanks. And the file Rg.xvg looks sound?
>
> Kind regards,
> Erik
>
> > On 23 Jan 2017, at 11:33, faride badalkhani 
> 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  >
> > 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  >
> >> 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-requ...@gromacs.org.
> >>
> >> --
> >> Gromacs Users mailing list
> >>
> >> * Please search the archive at http://www.gromacs.org/
> >> Support/Mailing_Lists/GMX-Users_List before posting!
> >>
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> >> send a mail to gmx-users-requ...@gromacs.org.
> >>
> > --
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Re: [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  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 
> 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 
>> 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-requ...@gromacs.org.
>> 
>> --
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>> 
>> * Please search the archive at http://www.gromacs.org/
>> Support/Mailing_Lists/GMX-Users_List before posting!
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Re: [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 
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 
> 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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> >
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Re: [gmx-users] Problem with the autocorrelation of Rg

[Erik Marklund]

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  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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[gmx-users] Problem with the autocorrelation of Rg

[faride badalkhani]

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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[gmx-users] Problem with the autocorrelation of Rg

[faride badalkhani]

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

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