Emanuel, The residence time which am referring is the water molecule residing on the particular location at a specific time.
Am not able to write a correct equation due to some character missing when typing from phone. Aiswarya Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it! -----Original Message----- From: aiswarya.pa...@gmail.com Date: Wed, 24 Aug 2011 16:13:05 To: Gromacs mail<gmx-users@gromacs.org> Reply-To: aiswarya.pa...@gmail.com Subject: Re: Antw: Re: [gmx-users] Hydrogen existence time Emanuel, The residence time which am referring is the water molecule residing on the particular location at a specific time. Am not able to write a correct equation due to small character missing when typing from phone. Aiswarya Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it! -----Original Message----- From: "Emanuel Peter" <emanuel.pe...@chemie.uni-regensburg.de> Date: Wed, 24 Aug 2011 16:16:37 To: <aiswarya.pa...@gmail.com>; <gmx-users@gromacs.org> Subject: Antw: Re: [gmx-users] Hydrogen existence time As I told you, you can calculate the self-diffusion coefficient by using g_msd. Following: Large diffusion-coeff. --> means : The residence time is low. Small diffusion-coeff. --> means : The residence time is large !!!! Mean-square-displacement means: Displacement of molecules per time. No displacement of molecule at all : if(msd == 0) means: Infinite residence time. So I say from my idiotic point of view: msd ~ residence time ( I still do not know what you mean with this because this is usually related to chemical reactors in engineering and NOT in protein simulation ) In your index-file you can index those molecules, which you need. Your equation does not make sense. >>> 24.08.11 16.01 Uhr >>> 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. 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.pa...@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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