Antw: Re: [gmx-users] calculate residence time for a protein complex

Emanuel Peter Emanuel.Peter at
Mon Aug 22 12:36:02 CEST 2011


You could calculate the number of H-bonds with the option -num .
Out of this x,y plot you have the possibility to calculate the correlation time by the H-bond
autocorrelation function < Number-of-Hbonds (t), Number-of-Hbonds (t_0) >.
This H-bond correlation-time could be equal to the residence time, because
it is equal to the average H-bond-existence time.
The correlation time is the time until the H-bond-correlation function shows no
correlated configuration any more. 

At least from my experience - 



>>> Mark Abraham  22.08.11 12.01 Uhr >>>
On 22/08/2011 6:22 PM, aiswarya pawar wrote:
> Hi,
> I have simulated a protein complex and now i would like to know the 
> residing water molecules between the protein complex. g_hbond and 
> trjorder helps in giving the number of hydrogen bonds and distance. 
> but is this the residence time calculation. please help me with this. 
> there few posts given in the archives regarding the residence time 
> which is not very clear to me. but will the residence time calculation 
> same for single protein and complex

Please do not cross-post requests for help to the mailing list and 
private individuals who have not advertised interest in such personal 
email. I do not even know what the definition of an H-bond residence 
time is. Hopefully somebody who does is reading the list.

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