Hi, Just need some advice regarding the following results I obtained while following the tutorial from this site, using a protein structure that I modelled using Modeller.
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/ 1. My output plot of RMSD doesn't converge. (From 0 - 0.4ns, its around 0.25nm, 0.4 - 0.7, around 0.3nm, 0.7 - 1.0ns, around 0.35). Does it mean that my EM wasn't properly done? Anyway, the EM did not reach the requested Fmax <100. 2. My graph for Radius of gyration from 800 - 1000ps shows a higher fluctuation than the ones from 0 - 800ps. Does it mean that the structure is not that stable? Please advice. (I followed exactly the steps in that tutorial. I'm new to Gromacs.) And of course, I neutralized my protein according to the charge needed. Not exactly following blindly from the tutorial. ;) Thank you very much in advance! :) Best wishes. -- View this message in context: http://gromacs.5086.n6.nabble.com/Output-for-rmsd-and-radius-of-gyration-doubts-tp5005881.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
