[gmx-users] Diffusion Coefficient calculations problem

[Dallas B. Warren]

> I performed 5 ns of simulation and I had the MSD x time curve nearly 
> linear until 1.3 ns and after this the linearity is lost (what is 
> natural since I´m performing the calculations for only one íon).

Stab in the dark here since you haven't gotten a reply yet, it isn't due to issues with the periodic boundary condition?  What happens if say you chop it up into 5 1ns blocks and calculate the msd for each one?  Is the linearity maintained?

Catch ya,

Dr. Dallas Warren
Lecturer
Department of Pharmaceutical Biology and Pharmacology
Victorian College of Pharmacy, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.warren at vcp.monash.edu.au
+61 3 9903 9073
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When the only tool you own is a hammer, every problem begins to resemble a nail.