Dear all,
Diffusion coefficient of water especially in porous medias like polymer is multiple of translational and rotational diffusion coefficient (DT + DR). In Gromacs we can have just translational diffusion coefficient using MSD. I want to calculate rotational diffusion coefficient in gromacs. How can I do for that? is there any specific module or I have to use other method?
Thank you very much
Dear Mohammad Rezayani,
Use this
https://manual.gromacs.org/archive/5.0/programs/gmx-rotacf.html
If my answer is helpful, please recommend it.
Based on my knowledge, direct evaluation of the rotational diffusion coefficient using GROMACS tools is not possible.
I would respectfully submit a related article in the attachment.
I hope you found this useful.
Dear Mehrdad Mohebi Shahpour Abadi
Thank you very much for your reply. I calculated rotational auto correlation function using gmx rotacf but I don't know how to find rotational diffusion coefficient. is there any special way to give me D directly like MSD? I mean how I can obtain DR from rotational auto correlation function?
Dear Seyedeh Tahereh Hosseini
Thank you very much for your reply.Unfortunately Yes!
One way to calculate DR is to plot MSAD(mean square angular displacement). This plot is the same as MSD but for angular movements. I think we have to write an script to achieve mentioned plot and calculate DR from slop which is a bit challenging!
Thanks again
The diffusion coefficient is determined by linear regression of the MSD, where, unlike for the normal output of D, the times are weighted according to the number of reference points, i.e. short times have a higher weight. Also when -beginfit=-1,fitting starts at 10% and when -endfit=-1, fitting goes to 90%. Using this option one also gets an accurate error estimate based on the statistics between individual molecules. Note that this diffusion coefficient and error estimate are only accurate when the MSD is completely linear between -beginfit and -endfit.
-type (no)
Compute diffusion coefficient in one direction: no, x, y, z
Article Molecular dynamics calculation of rotational diffusion coeff...
Dear Mehrdad Mohebi Shahpour Abadi
Thank you again for your reply and time. I got it completely.
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