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

[aiswarya pawar]

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 <
Emanuel.Peter at chemie.uni-regensburg.de> 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: * aiswarya.pawar at gmail.com
> *Date: *Wed, 24 Aug 2011 16:13:05 +0000
> *To: *Gromacs mail<gmx-users at gromacs.org>
> *ReplyTo: * aiswarya.pawar at gmail.com
> *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" <Emanuel.Peter at chemie.uni-regensburg.de>
> *Date: *Wed, 24 Aug 2011 16:16:37 +0200
> *To: *<aiswarya.pawar at gmail.com>; <gmx-users at gromacs.org>
> *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.
>
> >>> <aiswarya.pawar at gmail.com> 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, aiswarya.pawar at gmail.com 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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