I have simulated a box water molecules (1500 water molecules) using molecular dynamics method in NpT ensemble.
I got the time auto-correlation function (C(t) vs t, time) where its function line is parallel to x-axis. Which means the C(t) is zero.
I understand the water molecules are...
I wish to get some explanation on calculating velocity auto-correlation for water molecules in a box.
I have done 100 ns molecular dynamics simulation on 1445 water molecules in a box. Also I have calculated velocity for each water molecule in a frame. A frame contains 1445 water molecules...
When I calculate the autocorrelation function for 4000 frames with 1800 (tcorr) as for correlation time. I get negative values after about 600 frame and the graph approach towards tcorr=0.
In the literature it is stated as 'caging' effect. What is really means by caging effect...
Thanks for your reply.
I have few questions to ask relating to equation C(t_j) , to correct my understanding.
1) Does for every new t_j value (called as correlation time), which increases in step wise after each loop, the calculation needed to be done starting from frame 1 until...
I am posting this question here because my field of research is biophysics and i am doing molecular dynamics (MD) simulation on bilayer system.
Well, what I want is some explanations on calculating auto-correlation function using MD simulation data.
I have 4000 frames out...
It compiles. There is no problem. But when I execute it stops says error. The error indicates that the files (maximum_dist_001_064.dat) open ready.
That means in the first call of the main-data-file ( UNIT=100) it opens four files. Thay are
I am trying to write a loop to open four main-data-files. At each open of main-data-file, I want the loop to open another four sub-files and split the data from mail-data-file according to the creteria and dump into the four files. And the process goes on. That means I will have total of...
Thanks for your explanation.
You are correct sir. Actually what I want is the frequency histogram.
So in order to get this how the code should be?
I need help in this.
I appreciate your help in advance.
In this process, I have rewritten the code. Below is the code :-...
I may want to explain like this. Imagine we have x,y and z co-ordinate.
Lets say I have 10 values along x-axis and another 10 values along y-axis. The co-ordinates may look like this (x,y).
(1,4), (4,6), (2,6), (1,4), (2,6), (8,0), (1,4), (2,6), (1,4), (8,0)...
1) It is true that I can use the same variables for D and BB. But I used them just for my clarity purpose.
2) I used 1 * i since the bin size I used was 1. If the size is 0.5 than I need to replace the 1 with 0.5. This also just for my clarity purpose.
3) Actually what I want is, I...
Yea I have tried writing the code. It is as below:
integer, parameter :: D = 60 ! Number of data
integer, parameter :: BB=60 ! Number if bins
integer i, j, k
integer, dimension(1:D) :: xData, yData
integer, dimension(1:BB) :: bins
Hi FORTRAN experts,
I have two arrays of data, called data1.dat and data2.dat. each contains 60 data. What I want to do is to compare the data in each file and write the counting into bins. It goes like this. First, take the first data in data1.dat file and compare with the 60 data in...