<span class="Apple-style-span" style="font-family: 'times new roman'; font-size: 16px; border-collapse: collapse; ">Hi, all:<br>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:<br>
pull = umbrella<br>pull_geometry = distance<br>pull_vec1 = 0. 0. 1.<br>pull_dim = N N Y<br>pull_nstxout = 1000<br>pull_group0 = bilayer<br>pull_group1 = r3_P<br>
pull_k1 = 500<br>pull_rate1 = 0.001 ;nm/ps<br>integrator = md<br>dt = 0.002 ;ps<br>nsteps = 1000000<br>nstcomm = 1<br>comm_grps = DPP SOL<br>
nstxtcout = 100<br>nstlist = 10 <br>ns_type = grid<br>pbc = xyz<br>rlist = 1.0 <br>coulombtype = PME<br>rcoulomb = 1.0<br>
vdwtype = cut-off<br>rvdw = 1.0<br>ewald_rtol = 1e-5<br>optimize_fft = yes<br>tcoupl = Berendsen<br>tau_t = 0.1 0.1<br>tc_grps = DPP SOL<br>
ref_t = 323 323<br>pcoupl = Berendsen<br>pcoupltype = semiisotropic<br>tau_p = 1.0 1.0 <br>compressibility = 4.5e-5 4.5e-5<br>ref_p = 1.0 1.0 <br>
gen_vel = no<br>gen_temp = 323<br>gen_seed = 173529<br>constraints = all-bonds<br>constraint_algorithm = LINCS<br>lincs_order = 4<br><br>"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.<br>
<br>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?<br><br>Thanks.<br><br>dj</span>