I have to study diffusion by gromacs. I want to calculate full tensor of diffusion coefficients. I am using "g_msd -ten". But it is giving me only one value. I want to ask that my command is correct or not. If it is not then what is the exact command? I shall be thankful to you for this.
I don't see how that's possible. The -ten option, per the documentation, "writes the full MSD tensor for each group, the order in the output is: trace xx yy zz yx zx zy." Have you inspected the output file in a text editor and found only a single value, or have you just plotted the resulting file? If the latter, it's probably just a matter of plotting it correctly.
Oh ..Thanks Sir.. When I opened msd.xvg file then I got 8 columns. My problem is solved..
Please tell me,
How can i calculate the rotational diffusion coefficient/constant in gromacs.
Is there any other procedure available to do the rotational diffusion coefficient?
Thanks
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