I would like to know, weather I can use above script for truncated octahedren box or not. If not what are the changes should I make in the script. My second question is " what does this "good estimate of Dtransl" means or what is the range of good estimate."

Sorry, truncated octahedron is also not directly supported by this code. See previous posts in this thread for suggestions what to do. "good" means to within a few percent of the value that would be obtained using much longer times for the fit of the straight line to the MSD(t) curve.

Lennart Nilsson Karolinska Institutet Stockholm, Sweden

I am sorry that my question repeats something that was already wrote in a post above concerning the calculation of water diffusion coefficient based on MSD using coor anal command, but I am having trouble understanding the connection between the: - number of frames of a trajectory, - the frequency of saving coordinates in the trajectory, - the timestep used in the dynamics simulation, - the skip value used when reading the trajectory in coor anal command and - ncors value in coor anal. Are there any guidelines on selecting skip and ncors values depending on the analyzed trajectory features mentioned above (timestep, frequency of saving coordinates, number of frames of the analyzed trajectory)? Thank you!

A trajectory of 1 ns simulated with a 2 fs time step, and with coordinates saved every 500 steps (NSAVC 500 in the dynamics command) will contain 1000 frames (1000*0.002ps*500=1000ps=1ns). If you read this trajectory with NSKIP 2500 only every fifth frame (ie, every 5ps) will be read. NCORS is the number of points in the MSD(t) curve.

For the above trajectory the NCORS 100 and NSKIP 1000 would compute MSD(t) from t=0 to t= 100 * 1000 * 0.002ps=200ps

You have to compute MSD(t) to a large enough t that you clearly see the linear part. Using a small NSKIP increases the computational time, but this is usually not a problem.

Lennart Nilsson Karolinska Institutet Stockholm, Sweden

Thank you for your answer, I hope I understand it now. I calculated the MSD for the same trajectory using different combinations of ncors and nskip, each time charmm gives a different estimate of diffusion coefficient, of the order E00 to E-06, and even negative values. I want to ask how reliable this estimation is, or maybe I should plot the data and do the linear fit myself. I attached such a plot of MSD vs time and the plot is not that linear. Do you think it looks OK? Should I fit only the first 10 ps? In any way I fit it, I can not reproduce the estimated diffusion coefficient from charmm output. I would be very grateful if you could help me on this matter.

You should of course do the fit yourself, especially with curve like the one in the graph you attached, which does look a bit strange. Try to reproduce some published diffusion coefficient calculation for a box of water.

Last edited by lennart; 06/12/1802:47 PM.

Lennart Nilsson Karolinska Institutet Stockholm, Sweden