[gmx-users] Diffusion Coefficient calculations problem

[Alexandre Suman de Araujo]

I chopped the 10 ns simulation in 20 blocks of 500 ps, calculated the 
msd curve with trestart = 10 ps and calculated the mean value with the 
20 .xvg files. I had a good linear curve and good results.
Thank you Dallas.

Alexandre Suman de Araujo
asaraujo at if.sc.usp.br
UIN: 6194055
IFSC - USP - São Carlos - Brasil



Dallas B. Warren wrote:

>>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
>---------------------------------
>When the only tool you own is a hammer, every problem begins to resemble a nail.
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