<div>Hello guys, I have tried to calculate the PMF for a dimer in a </div><div>rectangular box of dimensions 3 x 3 x 7. However, the simulation </div><div>stops when the COM separation is above 1.49 (ie half </div><div>of the smallest dimension of the box. Since I am pulling along </div>
<div>the Z axis at a distance that would be up to 3.5 nm.</div><div><br></div><div>I've tried both pull_geometry, distance and direction, to try to get </div><div>around this, but I have not been successful. </div><div>
<br></div><div>Do I have to use the dimensions of the box as twice the COM </div><div>distance (in my case: 5 x 5 x 5; to give me r_max = 2.5nm)?</div><div><br></div><div>Some of you could give me a hand?</div><div><br></div>
<div><br></div><div>DIRECTION</div><div>pull = umbrella</div><div>pull_geometry = direction</div><div>pull_dim = Y Y Y</div><div>pull_group0 = mol_0</div><div>pull_group1 = mol_1</div>
<div>pull_rate1 = 0.01</div><div>pull_vec1 = 0.0 0.0 1.0</div><div>pull_k1 = 3000</div><div><br></div><div>DISTANCE</div><div>pull = umbrella</div><div>pull_geometry = distance</div>
<div>pull_dim = Y Y Y</div><div>pull_group0 = mol_0</div><div>pull_group1 = mol_1</div><div>pull_rate1 = 0.01</div><div>pull_vec1 = 0.0 0.0 0.0</div><div>
pull_k1 = 3000</div><div>_______________________________________<br>Eudes Eterno Fileti<br><div style="border-collapse:separate;font-family:arial"><span style="font-family:arial,sans-serif;font-size:13px;border-collapse:collapse">Instituto de Ciência e Tecnologia da UNIFESP<br>
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