Hi Justin, Thank you for your prompt reply! As this is my first approach to molecular dynamics, I still have lots of to understand but I'm constantly reading and trying to work things out. I predicted 2 structures, one using Modeller, and another one with I-Tasser. I followed your very informative tutorial for the approach of energy minimization and equilibration using Gromacs. My mistake for assuming that RMSD should fall within 0.1nm. I'm supposed to choose the best model to proceed with docking. Is it okay if I run just a 10ns simulation for both the predicted structure and then decide the best one by comparing the stability of the protein, from the output of the RMSD and radius of gyration?
Thank you in advance. Best wishes -- View this message in context: http://gromacs.5086.n6.nabble.com/Output-for-rmsd-and-radius-of-gyration-doubts-tp5005881p5006085.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing list gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
