Hi all ! I have a results of my MD and i have found a water molecule that was getting closer to my substrate on one frame of my dynamic. The distance is 3.4 A. Now I have to immobillize this water on this distance during the next step of MD by using a harmonic potential as the distance constraint, where the force constant is about 200 kcal/....I understand that i have to create an index file, it's ok, but my mdp is bad rather COM pulling in gromacs 4.0.5...
protein - my substrate LIN - my water ; COM PULLING ; Pull type: no, umbrella, constraint or constant_force pull = umbrella ; Pull geometry: distance, direction, cylinder or position pull_geometry = distance ; Select components for the pull vector. default: Y Y Y pull_dim = N N Y ; Cylinder radius for dynamic reaction force groups (nm) pull_r1 = 1 ; Switch from r1 to r0 in case of dynamic reaction force pull_r0 = 1.5 pull_constr_tol = 1e-06 pull_start = yes pull_nstxout = 10 pull_nstfout = 1 ; Number of pull groups pull_ngroups = 1 ; Group name, weight (default all 1), vector, init, rate (nm/ps), kJ/(mol*nm^2) pull_group0 = Protein pull_weights0 = pull_pbcatom0 = 0 pull_group1 = LIN pull_weights1 = pull_pbcatom1 = 0 pull_vec1 = 0.0 0.0 0.0 pull_init1 = 0.34 pull_rate1 = 0.0 pull_k1 = 837 pull_kB1 = 837 I've also tried cylynder geometry, changing pull_dim = ... but my water still goes out. Thank you for help!
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