Dear gromacs user, In order to simulate the PMF of a adsorbed short peptide on a solid surface, first I minimised and equlibrated(NVT and NPT) the system and then I did a 60 ns of production run in which the peptide fully adsorbed to the surface. I used these out put to pull away the peptide from the surface using below mdp file (to produced required trajectory for generating configuration): +++++++++++++++ title = C16-Slab-Water-Na integrator = md dt = 0.001 ; 1 fs nsteps = 10000000 ; 10 ns xtc-precision = 2000
nstenergy = 5000 nstlog = 5000 nstxout-compressed = 1000 nstxout = 1000 nstlist = 40 continuation = yes gen-vel = no ;gen-temp = 298.15 ;gen-seed = 173529 constraint-algorithm = lincs constraints = h-bonds cutoff-scheme = Verlet coulombtype = PME rcoulomb = 1.3 vdwtype = Cut-off rvdw = 1.3 DispCorr = EnerPres tcoupl = Nose-Hoover ;v-rescale ;berendsen tc-grps = Protein Non-Protein tau-t = 1.61 1.61 ref-t = 298.15 298.15 nhchainlength = 1 pbc = xyz pcoupl = no energygrps = Protein Slab Water_and_ions pull = yes pull-ngroups = 2 pull-ncoords = 1 pull-group1-name = Protein pull-group2-name = Slab pull-coord1-groups = 1 2 pull-coord1-type = umbrella pull-coord1-dim = N N Y pull-coord1-start = yes pull-coord1-rate = 0.001 ;;;0.007 pull-coord1-vec = 0.0 0.0 1.0 pull-coord1-geometry = direction-periodic pull-coord1-k = 500 ;;;1000 pull-print-components = Yes ++++++++++++++++ Although I do not use hard spring (500 and 1000) and fast pulling rate(0.001 and 0.007) but I do not know why the peptide suddenly pulled away from the slab in the second or third frame? Thanks. 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.