Dear All, I am running a SMD simulation (gromacs+plumed) pulling a ligand out of the enzyme. The parameters are, pulling velocity= 0.00005 per 1000 steps (2 ps, as in gromacs) force constant = 20920.0 kJ/mol/nm-2 CV from 0.3 nm to 1.7 nm
STEER CV 1 FROM 0.3 TO 1.7 KAPPA 20920.0 VEL 0.00005 So, I need to run a trajectory up to a time span of 56 ns [(2 ps /0.00005 nm)*1.4 nm]. part of nvt.mdp dt = 0.002 ; [ps] time step for integration nsteps = 28000000 ; maximum number of steps While running this simulation, I observe that after CV=1.0 (~23 ns), the graph becomes parallel to x-axis; the CV is not increasing (in principle, it should increase up to 1.7). What could be the issue in this SMD simulation? Is it that the velocity is too low, and the stiff-spring approximation is not getting obeyed? I appreciate your comments and suggestions. Thanks, Tarak -- 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.