Hi, all: I tried to pull a specific DPPC, say, r3, out of a pre-equilibrated bilayer into the water along the positive z axis. For the pull code parameters, I used: pull = umbrella pull_geometry = distance pull_vec1 = 0. 0. 1. pull_dim = N N Y pull_nstxout = 1000 pull_group0 = bilayer pull_group1 = r3_P pull_k1 = 500 pull_rate1 = 0.001 ;nm/ps integrator = md dt = 0.002 ;ps nsteps = 1000000 nstcomm = 1 comm_grps = DPP SOL nstxtcout = 100 nstlist = 10 ns_type = grid pbc = xyz rlist = 1.0 coulombtype = PME rcoulomb = 1.0 vdwtype = cut-off rvdw = 1.0 ewald_rtol = 1e-5 optimize_fft = yes tcoupl = Berendsen tau_t = 0.1 0.1 tc_grps = DPP SOL ref_t = 323 323 pcoupl = Berendsen pcoupltype = semiisotropic tau_p = 1.0 1.0 compressibility = 4.5e-5 4.5e-5 ref_p = 1.0 1.0 gen_vel = no gen_temp = 323 gen_seed = 173529 constraints = all-bonds constraint_algorithm = LINCS lincs_order = 4
"r3_P" corresponds to an index file that contains the phophorus group of r3, and "bilayer" corresponds to an index file that contains all the lipids except r3. I'm using GROMACS 4.0.3, but when I looked at the trajectory in VMD, the position of r3 is hardly moved. So what's the right way to pull this specific lipid into the water slab? Thanks. dj
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