[gmx-users] Hydrogen existence time

Mark Abraham Mark.Abraham at anu.edu.au
Thu Aug 25 01:48:21 CEST 2011

On 25/08/2011 12:00 AM, aiswarya.pawar at gmail.com wrote:
> Mark,
> The residence time equation goes like this-
> P(r)= function (N(t) - N(t+r))dt
> Where function(x-y) takes the value of 1 when x=y(x not equal to 0 and y not equal to 0) ie the site occupied and when x not equal to y or both x and y =0. N(t) index of water molecule found in the hydration site at time t.

So that's the autocorrelation of the existence function. Now you need a 
geometric criterion for existence. Note that g_hbond with 
well-constructed groups will calculate the autocorrelation of the 
existence function for an H-bond. See g_hbond -h.

g_dist, some scripting and g_analyse might be necessary for other criteria.


> Aiswarya
> ------Original Message------
> From: Mark Abraham
> To: Aiswarya Pawar
> Subject: Re: [gmx-users] Hydrogen existence time
> Sent: 24 Aug 2011 6:09 PM
> On 24/08/2011 10:31 PM, aiswarya.pawar at gmail.com wrote:
>> Any idea how can I calculate the residence time of water.
> First, seek define what you mean to calculate. If you can't write an
> equation down for it, you can't calculate it.
> Mark
> Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it!

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