Dear gromacs user, I was wondering how long normally should be the pulling time in one step before the final umbrella sampling? For instance in the Aβ42 protofibril umbrella sampling used in tutorial, the applied simulation times are as following referring to the original paper:
Production Normal MD: 100 ns Pulling time : 500 ps MD in each windows : 10 ns The second question is that can we limit the pulling region to pull away for example A from B as 3 nm in the pulling run(not in the final umbrella sampling)? Thanks, Regards, Alex -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
