[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.
Mark
>
> 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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