I want to calculate the diffusion coefficient of a single coarse-grained
polymer adsorbed on a wall with Gromacs 5.0.7, where the wall's type is 9-3 and
the density is set as 1. Firstly, I use the "gmx msd" command to calculate the
diffusion coefficient. The calculation error is very large and the results of
the parallel samples are always different. For example, I find the curve of
MSD-time is approximately linear, but the result of the "gmx msd" is incorrect,
<D> = 97.9395 Std. Dev. = 0.0000 Error = 0.0000
Fitting from 20 to 100 ps
D[ System] 99.2119 (+/- 31.8833) 1e-5 cm^2/s
Then, I try to use "gmx velacc" command to calculate the diffusion coefficient.
Similarly, the fluctuation of different parallel samples is still very large,
and I occasionally find the integral of the VACF is negative. In addition, I
try to change the “dt” and the “nstxout”, which can’t work. I have made
numerous attempts to solve this problem. Unfortunately, I have not succeeded.
I would be grateful if someone can help me solve this problem or provide
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