Antw: Re: [gmx-users] Hydrogen existence time

Emanuel Peter Emanuel.Peter at
Wed Aug 24 16:16:37 CEST 2011

As I told you, you can calculate the self-diffusion coefficient by using g_msd.

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
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 >>>

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.

------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 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.


Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it!
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