I was performing simulations on urea unfolding of protein. I performed one set of simulation for 50 ns with a velocity (set by gen_seed) and it went fine. Now when I am doing simulation using a different gen_seed from 10 to 20 ns many long bonds are formed. I could visualize them in vmd. Subsequently rmsd and radius of gyration plots also show the large change. But, energy is almost constant during the whole time period. Also after 20 ns this problem goes by itself and all bonds become normal. Why it could be so and how could I correct it. These bonds are so long that radius of gyration changes from 1.2 nm to 3.5 nm.
Thanking all in advance Siddhant -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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
