Hi, my system is constructed of 2 parallel plates in a box with solvent. each plate is made of 36 atoms which are positively charged on one of them (SRP) and negatively charged on the other plate (SRN).
i want to perform a simulation with umbrella sampling between the 2 so i defined the pulling section parameters in the .mdp parameter file as following: ; 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 = Y Y 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 = no pull_nstxout = 10 pull_nstfout = 1 ; Number of pull groups pull_ngroups = 2 ; Group name, weight (default all 1), vector, init, rate (nm/ps), kJ/(mol*nm^2) pull_group0 = SRP pull_weights0 = 1 pull_pbcatom0 = 0 pull_group1 = SRN pull_weights1 = 1 pull_pbcatom1 = 0 pull_vec1 = 0.0 1.0 0.0 pull_init1 = 1.5 pull_rate1 = 0 pull_k1 = 1 pull_kB1 = 0 when proccesing the file with grompp i get the following error: *Fatal error: Number of weights (1) for pull group 0 'SRP' does not match the number of atoms (36)* is someone recognizing my mistake? does someone has an experience with umbrella sampling in GROMACS? thanks' amir * *
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