HI
However, since I want to pull the protein for a long distance, I should > gradually change the equilibrium length, and I have no idea how to > dynamically change the "pull-coord1-init" during SMD simulation. Or do I > have to restart the simulation with a new .mdp file with different > "pull-coord1-init" for each step? > > > To change the pulling coordination during the simulation you can apply a rate. pull-coord1-rate [nm/ps] is the rate of change of the reference position I suggest to combine with pull-coord1-init [nm] (that is the reference distance at t=0). (see http://manual.gromacs.org/documentation/current/user-guide/mdp-options.html?highlight=freeze%20groups#com-pulling ) This is also useful to generate starting configurations (at defined distance values) for the umbrella sampling windows. Best regards Alessandra > Best regards, > W > -- > 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. -- 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.
