Dear Emanuel, Thank you so much for the pseudo-code, it made me understand the flow. 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.
Thanks, Aiswarya On Thu, Aug 25, 2011 at 1:53 PM, Emanuel Peter < [email protected]> wrote: > Hello Aiswarya, > > Your program should look like this, in pseudo-code: > > pseudo-code: > > do n_frames_of_your_trajectory > > 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) > > processing the atm-pair.out list and write them into an index file : 1.ndx, > with each water in one group > > take just these atoms and residues, which are at your specific distance at > your 'location' > > do > > measure the angle in relation to your protein for this frame for each > specified water > > g_angle -f traj.trr -s .tpr -n 1.ndx -b (one frame of your trajectory) -e > (the same frame) > > enddo > > read the angles from the output > > take just the one water with specific angle out of your list. > > (By using g_mindist -d , and g_angle you specify one specific point in > relation to your protein) > (By using -b and -e you specify one specific time) > > save the residue number of this water and your frame > > calculate the time of this frame > > enddo > > now you have an array of residue numbers at this particular location for > each time > > analyse this array, then you know the maximum frame-time of one > water-molecule at this specific location. > You will not get any information about one particular time - just an > average. > This must be your residence time. > > Your application needs some little programming. > > > >>> ** 24.08.11 18.14 Uhr >>> > 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! > ------------------------------ > *From: * [email protected] > *Date: *Wed, 24 Aug 2011 16:13:05 +0000 > *To: *Gromacs mail<[email protected]> > *ReplyTo: * [email protected] > *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! > ------------------------------ > *From: * "Emanuel Peter" <[email protected]> > *Date: *Wed, 24 Aug 2011 16:16:37 +0200 > *To: *<[email protected]>; <[email protected]> > *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. > > >>> <[email protected]> 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, [email protected] 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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