Hi Justin, I tried running the simulation for 10ns and this time, my RMSD graph shows a stable fluctuation of 0.45nm from 2.5ns to 10ns. The radius of gyration shows stable fluctuation from 4ns to 10ns around 2.46nm. My doubt is, shouldn't the RMSD be fluctuating at 0.1nm? Does it mean that my structure is not stable? Or do I need to run more than 10ns of simulation?
Please advice. :( I attached a screenshot of the graph in case I didn't explain it well. g_rms http://postimage.org/image/f4bkobtx9/ g_gyrate http://postimage.org/image/gd86i2jpj/ Thanking you in advance. Best wishes -- View this message in context: http://gromacs.5086.n6.nabble.com/Output-for-rmsd-and-radius-of-gyration-doubts-tp5005881p5006080.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
