Dear all I cannot understand the explanations about settings of pull code in the gmx 4.
Take a example, there are two particles in the system, and I want to reproduce the LJ potential using "umbrella sampling". The settings in gmx 3.3.3 is following: ===================== .......... runtype = umbrella ngroups = 1 group_1 = Arg2 reference_group = Arg1 ...... pulldim = N N Y K1 = 700 POS1 = 0 0 1 ====================== But I don't know how to set it in gmx 4 Following is the settings in gmx 4: ====================== ; COM PULLING ; Pull type: no, umbrella, constraint or constant_force pull = umbrella ; ---> "runtype" in gmx 3.3.3 ; 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 ; ---> "pulldim" in gmx 3.3.3 ; 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 = 1 ; ---> "ngroups" in gmx 3.3.3 ; Group name, weight (default all 1), vector, init, rate (nm/ps), kJ/(mol*nm^2) pull_group0 = Arg2 ; ---> "reference_group" in gmx 3.3.3 pull_weights0 = pull_pbcatom0 = 0 pull_group1 = Arg1 ; ---> "group1" in gmx 3.3.3 pull_weights1 = pull_pbcatom1 = 0 pull_vec1 = 0.0 0.0 0.0 pull_init1 = 0.0 pull_rate1 = 0 pull_k1 = 700 ; ---> "k1" in gmx 3.3.3 pull_kB1 = 0 ====================== if right, which parameter corresponds with "pos1" in gmx3.3.3? I must apologize in advance if I miss some details in the manual. Thank you very much Li Yang _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
