<html><head><meta http-equiv=Content-Type content="text/html; charset=Windows-1252"><META name="Author" content="Novell GroupWise WebAccess"></head><body style='font-family: Tahoma, sans-serif; font-size: 13px; '>As I told you, you can calculate the self-diffusion coefficient by using g_msd.<br>Following:<br><br>Large diffusion-coeff. --> means : The residence time is low.<br>Small diffusion-coeff. --> means : The residence time is large !!!!<br><br>Mean-square-displacement means: Displacement of molecules per time.<br>No displacement of molecule at all : if(msd == 0) means: Infinite residence time.<br>So I say from my idiotic point of view: msd ~ residence time ( I still do not know what you mean with this because<br>this is usually related to chemical reactors in engineering and NOT in protein simulation ) <br>In your index-file you can index those molecules, which you need.<br>Your equation does not make sense. <br><br>>>> <aiswarya.pawar@gmail.com> 24.08.11 16.01 Uhr >>><br>Mark,<br><br>The residence time equation goes like this-<br><br>P(r)= function (N(t) - N(t+r))dt<br><br>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.<br><br>Aiswarya<br>------Original Message------<br>From: Mark Abraham<br>To: Aiswarya Pawar<br>Subject: Re: [gmx-users] Hydrogen existence time<br>Sent: 24 Aug 2011 6:09 PM<br><br>On 24/08/2011 10:31 PM, aiswarya.pawar@gmail.com wrote:<br>> Any idea how can I calculate the residence time of water.<br><br>First, seek define what you mean to calculate. If you can't write an <br>equation down for it, you can't calculate it.<br><br>Mark<br><br>Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it!</body></html>