[gmx-users] Diffusion Coefficient calculations problem

Alexandre Suman de Araujo asaraujo at if.sc.usp.br
Thu Feb 2 16:35:33 CET 2006

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
>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.
>gmx-users mailing list    gmx-users at gromacs.org
>Please don't post (un)subscribe requests to the list. Use the 
>www interface or send it to gmx-users-request at gromacs.org.
>Can't post? Read http://www.gromacs.org/mailing_lists/users.php

More information about the gromacs.org_gmx-users mailing list