Hello everyone,
I was wondering if anyone knew how to plot and visualize the convergence of the diffusion coefficient for a single solute molecule, which in my case is glucose? So far, I have been trying to achieve this by using the diffusion action command in CPPTRAJ which utilizes linear regression between the mean squared displacement (MSD) and time, but I haven't been able to achieve convergence no matter what I try. Another major question that arises here is how do you correctly sample the diffusion coefficient to see convergence? For example, if you have a 1 us simulation, do you:
1. calculate D from 0 to 50 ns, then 0 to 100 ns, then 0 to 150 ns, and so on?
or
2. calculate D from 0 to 50 ns, then 50 to 100 ns, then 100 to 150 ns, and so on?
I've also noticed in the CPPTRAJ manual that using the MSD to calculate diffusion coefficients is only possible when averaged over many copies of the same molecule, which may be the main problem here.
Any advice would be welcome.
Thanks,
Sam
Postdoctoral Fellow
Complex Carbohydrate Research Center
University of Georgia
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Received on Wed Jan 03 2024 - 11:30:03 PST
