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

[Emanuel Peter]

The number of frames is in your mdp-file.
nstxout = frequency of output (timestep when it writes out one frame)
dt         = timestep

time of frame = number_of_frame * nstxout * dt

With programming you have to learn one certain programming-language.
I cannot help you with learning programming - this at least you have to do
yourself.

>>what programming should be applied and what for

I would suggest you to learn C or Fortran-coding.
You also could use a script-language, like bash.
A theoretician must be able to do some little programming. 

If you want to do that 1000.000 times by hand, you can do it.
You also could integrate the equations of motion by hand for your trajectory.

>>> aiswarya pawar  25.08.11 10.54 Uhr >>>
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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