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