Re: [gmx-users] autocorrelation function and residence time

[Tasneem Kausar]

Thank You

On Fri, Sep 22, 2017 at 1:35 PM, Erik Marklund 
wrote:

> Dear Tsaneem,
>
> Negative values don’t signify lack of correlation, but anticorrelation.
> Also, by omitting negative values you introduce a slight bias in your fit
> towards longer half-life.
>
> Kind regards,
> Erik
> __
> Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow
> Department of Chemistry – BMC, Uppsala University
> +46 (0)18 471 4539
> erik.markl...@kemi.uu.se
>
> On 22 Sep 2017, at 06:18, Tasneem Kausar  mailto:tasneemkausa...@gmail.com>> wrote:
>
> Thank you for reply
>
> I read the references and I know that one of the columns of g_hbond output
> is without subtraction
> and the value ranges between 0 to 1. The only help I need is that can I
> fit the curve of the first column (which has negative value) and neglect
> the range of curve of negative part while fitting to get the exponential
> parameters of the curve. This seems to me reasonable only for getting
> information parameter as negative ACF value mean no correlation parameter.
>
> Any help will be appreciated.
>
> Thanks in Advance.
>
> On Thu, Sep 21, 2017 at 2:54 PM, Erik Marklund  mailto:erik.markl...@kemi.uu.se>>
> wrote:
>
> Dear Tasneem,
>
> Quite often ACF calculations involve subtraction of the average signal,
> and this normally renders some negative values in the ACF. It’s been a bit
> too long since I dealt with the gmx hbond code, but I suspect that is what
> is going on here. I suggest reading the references that gmx hbond mentions,
> where the four quantities in the output are defined.
>
> Kind regards,
> Erik
> __
> Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow
> Department of Chemistry – BMC, Uppsala University
> +46 (0)18 471 4539
> erik.markl...@kemi.uu.se erik.markl...@kemi.uu.se>
>
> On 21 Sep 2017, at 11:12, Tasneem Kausar  mailto:tasneemkausa...@gmail.com><
> mailto:tasneemkausa...@gmail.com>> wrote:
>
> Still waiting for suggestions.
>
> On Wed, Sep 20, 2017 at 9:42 AM, Tasneem Kausar  
> >
> wrote:
>
> Dear all
>
> I want to calculate residence time of interface water molecules at protein
> interface. I am using Gromacs-4.6.4.
> I am using using following command
> g_hbond -s protein.tpr -f protein.xtc -b 2000 -n proein.ndx -ac
> protein_ac.xvg -contact
> In the index file there are protein interface residues and  8 water
> molecule that are present at the protein interface. I have selected protein
> interface and 8 water for calculation. In the output of autocorrelation
> there are four y axis columns. I came through reply of Erik. He mentioned
> the effect of periodic boundary condition on the output. In my case first y
> axis has several negative values. I want to do an exponential fit with
> function y=exp(-(x/t)^n) to obtain value of t and b. Can we skip the
> negative values of the output file? If yes what is the reason to do that.
> If I am wrong please suggest me to do the right way to obtain residence
> time.
>
>
> Thanks in Advance
>
> Tasneem Kausar
>
>
>
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Re: [gmx-users] autocorrelation function and residence time

[Erik Marklund]

Dear Tsaneem,

Negative values don’t signify lack of correlation, but anticorrelation. Also, 
by omitting negative values you introduce a slight bias in your fit towards 
longer half-life.

Kind regards,
Erik
__
Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow
Department of Chemistry – BMC, Uppsala University
+46 (0)18 471 4539
erik.markl...@kemi.uu.se

On 22 Sep 2017, at 06:18, Tasneem Kausar 
mailto:tasneemkausa...@gmail.com>> wrote:

Thank you for reply

I read the references and I know that one of the columns of g_hbond output
is without subtraction
and the value ranges between 0 to 1. The only help I need is that can I
fit the curve of the first column (which has negative value) and neglect
the range of curve of negative part while fitting to get the exponential
parameters of the curve. This seems to me reasonable only for getting
information parameter as negative ACF value mean no correlation parameter.

Any help will be appreciated.

Thanks in Advance.

On Thu, Sep 21, 2017 at 2:54 PM, Erik Marklund 
mailto:erik.markl...@kemi.uu.se>>
wrote:

Dear Tasneem,

Quite often ACF calculations involve subtraction of the average signal,
and this normally renders some negative values in the ACF. It’s been a bit
too long since I dealt with the gmx hbond code, but I suspect that is what
is going on here. I suggest reading the references that gmx hbond mentions,
where the four quantities in the output are defined.

Kind regards,
Erik
__
Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow
Department of Chemistry – BMC, Uppsala University
+46 (0)18 471 4539
erik.markl...@kemi.uu.se

On 21 Sep 2017, at 11:12, Tasneem Kausar 
mailto:tasneemkausa...@gmail.com><
mailto:tasneemkausa...@gmail.com>> wrote:

Still waiting for suggestions.

On Wed, Sep 20, 2017 at 9:42 AM, Tasneem Kausar 
mailto:tasneemkausa...@gmail.com>
>
wrote:

Dear all

I want to calculate residence time of interface water molecules at protein
interface. I am using Gromacs-4.6.4.
I am using using following command
g_hbond -s protein.tpr -f protein.xtc -b 2000 -n proein.ndx -ac
protein_ac.xvg -contact
In the index file there are protein interface residues and  8 water
molecule that are present at the protein interface. I have selected protein
interface and 8 water for calculation. In the output of autocorrelation
there are four y axis columns. I came through reply of Erik. He mentioned
the effect of periodic boundary condition on the output. In my case first y
axis has several negative values. I want to do an exponential fit with
function y=exp(-(x/t)^n) to obtain value of t and b. Can we skip the
negative values of the output file? If yes what is the reason to do that.
If I am wrong please suggest me to do the right way to obtain residence
time.


Thanks in Advance

Tasneem Kausar



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Re: [gmx-users] autocorrelation function and residence time

[Tasneem Kausar]

Thank you for reply

I read the references and I know that one of the columns of g_hbond output
is without subtraction
 and the value ranges between 0 to 1. The only help I need is that can I
fit the curve of the first column (which has negative value) and neglect
the range of curve of negative part while fitting to get the exponential
parameters of the curve. This seems to me reasonable only for getting
information parameter as negative ACF value mean no correlation parameter.

Any help will be appreciated.

Thanks in Advance.

On Thu, Sep 21, 2017 at 2:54 PM, Erik Marklund 
wrote:

> Dear Tasneem,
>
> Quite often ACF calculations involve subtraction of the average signal,
> and this normally renders some negative values in the ACF. It’s been a bit
> too long since I dealt with the gmx hbond code, but I suspect that is what
> is going on here. I suggest reading the references that gmx hbond mentions,
> where the four quantities in the output are defined.
>
> Kind regards,
> Erik
> __
> Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow
> Department of Chemistry – BMC, Uppsala University
> +46 (0)18 471 4539
> erik.markl...@kemi.uu.se
>
> On 21 Sep 2017, at 11:12, Tasneem Kausar  mailto:tasneemkausa...@gmail.com>> wrote:
>
> Still waiting for suggestions.
>
> On Wed, Sep 20, 2017 at 9:42 AM, Tasneem Kausar  >
> wrote:
>
> Dear all
>
> I want to calculate residence time of interface water molecules at protein
> interface. I am using Gromacs-4.6.4.
> I am using using following command
> g_hbond -s protein.tpr -f protein.xtc -b 2000 -n proein.ndx -ac
> protein_ac.xvg -contact
> In the index file there are protein interface residues and  8 water
> molecule that are present at the protein interface. I have selected protein
> interface and 8 water for calculation. In the output of autocorrelation
> there are four y axis columns. I came through reply of Erik. He mentioned
> the effect of periodic boundary condition on the output. In my case first y
> axis has several negative values. I want to do an exponential fit with
> function y=exp(-(x/t)^n) to obtain value of t and b. Can we skip the
> negative values of the output file? If yes what is the reason to do that.
> If I am wrong please suggest me to do the right way to obtain residence
> time.
>
>
> Thanks in Advance
>
> Tasneem Kausar
>
>
>
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Re: [gmx-users] autocorrelation function and residence time

[Erik Marklund]

Dear Tasneem,

Quite often ACF calculations involve subtraction of the average signal, and 
this normally renders some negative values in the ACF. It’s been a bit too long 
since I dealt with the gmx hbond code, but I suspect that is what is going on 
here. I suggest reading the references that gmx hbond mentions, where the four 
quantities in the output are defined.

Kind regards,
Erik
__
Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow
Department of Chemistry – BMC, Uppsala University
+46 (0)18 471 4539
erik.markl...@kemi.uu.se

On 21 Sep 2017, at 11:12, Tasneem Kausar 
mailto:tasneemkausa...@gmail.com>> wrote:

Still waiting for suggestions.

On Wed, Sep 20, 2017 at 9:42 AM, Tasneem Kausar 
mailto:tasneemkausa...@gmail.com>>
wrote:

Dear all

I want to calculate residence time of interface water molecules at protein
interface. I am using Gromacs-4.6.4.
I am using using following command
g_hbond -s protein.tpr -f protein.xtc -b 2000 -n proein.ndx -ac
protein_ac.xvg -contact
In the index file there are protein interface residues and  8 water
molecule that are present at the protein interface. I have selected protein
interface and 8 water for calculation. In the output of autocorrelation
there are four y axis columns. I came through reply of Erik. He mentioned
the effect of periodic boundary condition on the output. In my case first y
axis has several negative values. I want to do an exponential fit with
function y=exp(-(x/t)^n) to obtain value of t and b. Can we skip the
negative values of the output file? If yes what is the reason to do that.
If I am wrong please suggest me to do the right way to obtain residence
time.


Thanks in Advance

Tasneem Kausar



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Re: [gmx-users] autocorrelation function and residence time

[Tasneem Kausar]

Still waiting for suggestions.

On Wed, Sep 20, 2017 at 9:42 AM, Tasneem Kausar 
wrote:

> Dear all
>
> I want to calculate residence time of interface water molecules at protein
> interface. I am using Gromacs-4.6.4.
>  I am using using following command
> g_hbond -s protein.tpr -f protein.xtc -b 2000 -n proein.ndx -ac
> protein_ac.xvg -contact
> In the index file there are protein interface residues and  8 water
> molecule that are present at the protein interface. I have selected protein
> interface and 8 water for calculation. In the output of autocorrelation
> there are four y axis columns. I came through reply of Erik. He mentioned
> the effect of periodic boundary condition on the output. In my case first y
> axis has several negative values. I want to do an exponential fit with
> function y=exp(-(x/t)^n) to obtain value of t and b. Can we skip the
> negative values of the output file? If yes what is the reason to do that.
> If I am wrong please suggest me to do the right way to obtain residence
> time.
>
>
> Thanks in Advance
>
> Tasneem Kausar
>
>
>
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[gmx-users] autocorrelation function and residence time

[Tasneem Kausar]

Dear all

I want to calculate residence time of interface water molecules at protein
interface. I am using Gromacs-4.6.4.
 I am using using following command
g_hbond -s protein.tpr -f protein.xtc -b 2000 -n proein.ndx -ac
protein_ac.xvg -contact
In the index file there are protein interface residues and  8 water
molecule that are present at the protein interface. I have selected protein
interface and 8 water for calculation. In the output of autocorrelation
there are four y axis columns. I came through reply of Erik. He mentioned
the effect of periodic boundary condition on the output. In my case first y
axis has several negative values. I want to do an exponential fit with
function y=exp(-(x/t)^n) to obtain value of t and b. Can we skip the
negative values of the output file? If yes what is the reason to do that.
If I am wrong please suggest me to do the right way to obtain residence
time.


Thanks in Advance

Tasneem Kausar
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