[gmx-users] autocorrelation function and residence time

[Tasneem Kausar]

Thank You

On Fri, Sep 22, 2017 at 1:35 PM, Erik Marklund <erik.marklund at kemi.uu.se>
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.marklund at kemi.uu.se<mailto:erik.marklund at kemi.uu.se>
>
> On 22 Sep 2017, at 06:18, Tasneem Kausar <tasneemkausar12 at gmail.com<
> mailto:tasneemkausar12 at 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 <erik.marklund at kemi.uu.se<
> mailto:erik.marklund at 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.marklund at kemi.uu.se<mailto:erik.marklund at kemi.uu.se><mailto:
> erik.marklund at kemi.uu.se>
>
> On 21 Sep 2017, at 11:12, Tasneem Kausar <tasneemkausar12 at gmail.com<
> mailto:tasneemkausar12 at gmail.com><
> mailto:tasneemkausar12 at gmail.com>> wrote:
>
> Still waiting for suggestions.
>
> On Wed, Sep 20, 2017 at 9:42 AM, Tasneem Kausar <tasneemkausar12 at gmail.com
> <mailto:tasneemkausar12 at gmail.com>
> <mailto:tasneemkausar12 at 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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