<div>Hello everybody, I have used pull code to separate two molecules in water.</div><div>The idea is to generate initial configurations for umbrella sampling.</div><div>Initially I tried to use pull_geometry=distance. I noticed that the vector connecting </div>
<div>the two molecules are not remained on the main axis of the box (z). Then I realized </div><div>that using pull_geometry=direction (with pull_vec1= 0 0 1) I could keep this distance </div><div>on the z axis. However, the result of the pulling was exactly the same as with </div>
<div>pull_geometry=distance, ie, as the molecule moves away from the reference molecule the </div><div>distance of separation does not remain on the z axis, as I wish.</div><div><br></div><div>The protocol used was as follows:</div>
<div>pull = umbrella</div><div>pull_geometry = direction</div><div>pull_dim = N N Y</div><div>pull_ngroups = 1</div><div>pull_group0 = mol_0</div><div>
pull_weights0 = </div><div>pull_pbcatom0 = 0</div><div>pull_group1 = mol_1</div><div>pull_weights1 = </div><div>pull_pbcatom1 = 0</div><div>pull_vec1 = 0.0 0.0 1.0</div>
<div>pull_init1 = 0.0</div><div>pull_rate1 = 0.01</div><div>pull_k1 = 1000</div><div><br></div><div>Someone could direct me to where I am wrong?</div><div>Bests</div><div>eef</div>
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