<html><head><meta http-equiv=Content-Type content="text/html; charset=iso-8859-1"><META name="Author" content="Novell GroupWise WebAccess"></head><body style='font-family: Tahoma, sans-serif; font-size: 13px; '>The number of frames is in your mdp-file.<br>nstxout = frequency of output (timestep when it writes out one frame)<br>dt = timestep<br><br>time of frame = number_of_frame * nstxout * dt<br><br>With programming you have to learn one certain programming-language.<br>I cannot help you with learning programming - this at least you have to do yourself.<br><br>
>>what programming should be applied and what for<br><br>I would suggest you to learn C or Fortran-coding.<br>You also could use a script-language, like bash.<br>A theoretician must be able to do some little programming. <br><br>If you want to do that 1000.000 times by hand, you can do it.<br>You also could integrate the equations of motion by hand for your trajectory.<br><br>>>> aiswarya pawar <aiswarya.pawar@gmail.com> 25.08.11 10.54 Uhr >>><br>
Dear Emanuel,<br><br>Thank you so much for the pseudo-code, it made me understand the flow.<br>from your code it shows that, your using distance and angle as an criteria to select a water molecule in just one one time frame. right?? i didnt get how to calculate the time of the frame. what programming should be applied and what for.<br>
<br>Thanks,<br>Aiswarya<br><br><div class="gmail_quote">On Thu, Aug 25, 2011 at 1:53 PM, Emanuel Peter <span dir="ltr"><<a href="mailto:Emanuel.Peter@chemie.uni-regensburg.de">Emanuel.Peter@chemie.uni-regensburg.de</a>></span> wrote:<br>
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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.<div class="im"><br><br>>>> <u></u> 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</div><p>Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it!</p><hr><div class="im"><div><b>From: </b> <a href="mailto:aiswarya.pawar@gmail.com" target="_blank">aiswarya.pawar@gmail.com</a>
</div><div><b>Date: </b>Wed, 24 Aug 2011 16:13:05 +0000</div><div><b>To: </b>Gromacs mail<<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>></div><div><b>ReplyTo: </b> <a href="mailto:aiswarya.pawar@gmail.com" target="_blank">aiswarya.pawar@gmail.com</a>
</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</div><p>Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it!</p><hr><div class="im">
<div><b>From: </b> "Emanuel Peter" <<a href="mailto:Emanuel.Peter@chemie.uni-regensburg.de" target="_blank">Emanuel.Peter@chemie.uni-regensburg.de</a>>
</div><div><b>Date: </b>Wed, 24 Aug 2011 16:16:37 +0200</div><div><b>To: </b><<a href="mailto:aiswarya.pawar@gmail.com" target="_blank">aiswarya.pawar@gmail.com</a>>; <<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>></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>>>> <<a href="mailto:aiswarya.pawar@gmail.com" target="_blank">aiswarya.pawar@gmail.com</a>> 24.08.11 16.01 Uhr >>><br></div><div class="im">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></div><div class="im">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, <a href="mailto:aiswarya.pawar@gmail.com" target="_blank">aiswarya.pawar@gmail.com</a> 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!<u></u></div>
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