<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; '>
Hello Aiswarya,<br><br>Your program should look like this, in pseudo-code:<br><br>pseudo-code:<br><br>do n_frames_of_your_trajectory<br><br>g_mindist -f traj.trr -s .tpr -n (your_protein (first-group) , your_solvent (second-group)).ndx -o atm-pair.out -d your-distance-value -b (one frame of your trajectory) -e (the same frame)<br><br>processing the atm-pair.out list and write them into an index file : 1.ndx, with each water in one group<br><br>take just these atoms and residues, which are at your specific distance at your 'location'<br><br>do<br><br>measure the angle in relation to your protein for this frame for each specified water <br><br>g_angle -f traj.trr -s .tpr -n 1.ndx -b (one frame of your trajectory) -e (the same frame)<br><br>enddo<br><br>read the angles from the output<br><br>take just the one water with specific angle out of your list.<br><br>(By using g_mindist -d , and g_angle you specify one specific point in relation to your protein)<br>(By using -b and -e you specify one specific time)<br><br>save the residue number of this water and your frame<br><br>calculate the time of this frame <br><br>enddo<br><br>now you have an array of residue numbers at this particular location for each time<br><br>analyse this array, then you know the maximum frame-time of one water-molecule at this specific location.<br>You will not get any information about one particular time - just an average.<br>This must be your residence time.<br><br>Your application needs some little programming.<br><br>>>> <aiswarya.pawar@gmail.com> 24.08.11 18.14 Uhr >>><br>
Emanuel,<br><br>The residence time which am referring is the water molecule residing on the particular location at a specific time.<br><br>Am not able to write a correct equation due to some character missing when typing from phone.<br><br>Aiswarya<p>Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it!</p><hr><div><b>From: </b> aiswarya.pawar@gmail.com
</div><div><b>Date: </b>Wed, 24 Aug 2011 16:13:05 +0000</div><div><b>To: </b>Gromacs mail<gmx-users@gromacs.org></div><div><b>ReplyTo: </b> aiswarya.pawar@gmail.com
</div><div><b>Subject: </b>Re: Antw: Re: [gmx-users] Hydrogen existence time</div><div><br></div>Emanuel,<br><br>The residence time which am referring is the water molecule residing on the particular location at a specific time.<br><br>Am not able to write a correct equation due to small character missing when typing from phone.<br><br>Aiswarya<p>Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it!</p><hr><div><b>From: </b> "Emanuel Peter" <Emanuel.Peter@chemie.uni-regensburg.de>
</div><div><b>Date: </b>Wed, 24 Aug 2011 16:16:37 +0200</div><div><b>To: </b><aiswarya.pawar@gmail.com>; <gmx-users@gromacs.org></div><div><b>Subject: </b>Antw: Re: [gmx-users] Hydrogen existence time</div><div><br></div>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!</aiswarya.pawar@gmail.com></body></html>