Hello, I'm trying to do constrained simulations of a system consisting of two solvated proteins separated at a given distance. Inside the box there are also around 14.000 water molecules. At the bottom there is the .pdo file (I'm using gromacs 3.3.3).
However, it seems as it does not work. At the beginning of a simulation of 1.5 ns this was the positions of the centers of mass of the two proteins: Initial coordinates center of mass: 3.100 2.983 3.377 Initial coordinates center of mass: 2.972 3.006 8.821 After 1.5 ns: Initial coordinates center of mass: 3.040 3.690 2.740 Initial coordinates center of mass: 2.976 3.005 8.828 The distance changed from 5.445 nm to 6.127 nm. What's wrong? I appreciate your advice on this issue. Thank you very much in advance, Joseph ; GENERAL verbose = no Skip steps = 1 ; Runtype: afm, constraint, umbrella runtype = constraint ; Groups to be pulled group_1 = protein_a ; The group for the reaction force. reference_group = protein_b ; Weights for all atoms in each group (default all 1) weights_1 = weights_2 = weights_3 = weights_4 = reference_weights = ; Ref. type: com, com_t0, dynamic, dynamic_t0 reftype = com_t0 ; Use running average for reflag steps for com calculation reflag = 1 ; Select components for the pull vector. default: Y Y Y pulldim = Y Y Y ; DYNAMIC REFERENCE GROUP OPTIONS ; Cylinder radius for dynamic reaction force groups (nm) r = 1 ; Switch from r to rc in case of dynamic reaction force rc = 1.2 ; Update frequency for dynamic reference groups (steps) update = 1 ; CONSTRAINT RUN OPTIONS ; Direction, default: 0 0 0, no direction constraint_direction = 1.0 1.0 1.0 ; Rate of chance of the constraint length, in nm/ps ;constraint_rate = 0.0 ; Tolerance of constraints, in nm constraint_tolerance = 1e-06
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