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<p>Sorry, I want to ask the same question I had a week ago. I need your advice in COM PULL. </p>
<p>This is a part of article which describes methodology "...with respect to the atomic distance between the carbonyl carbon of the substrate and the oxygen atom of the identified nucleophilic water, a constrained MD simulation was performed to investigate the mechanisms of the approach of the water molecule. This simulation was started by using a harmonic potential as the distance constraint, where the force constant was set to 5 kcal/mol å2. When the atomic distance was not reduced any further, despite the presence of the harmonic potential in the MD simulation (at about 470 ps), the force constant was increased up to 200 kcal/mol å2; this was exploited to mimic the first phase of a nucleophilic attack..all together about 1ns"</p>
<p>and</p>
<p>"The atomic distance is 3.4 A, suggesting that this water molecule acts as a nucleophile in the post-transfer editing reaction.."</p>
<p>I have to reduce distance between oxygen of H2O and carbon during simulation, but H2O must be free enough for revolution around C. Index file is ready for it. This is part of mdp.</p>
<p>; COM PULLING </p>
<p>; Pull type: no, umbrella, constraint or constant_force</p>
<p>pull = umbrella</p>
<p>; Pull geometry: distance, direction, cylinder or position</p>
<p>pull_geometry = distance</p>
<p>; Select components for the pull vector. default: Y Y Y</p>
<p>pull_dim = Y Y Y</p>
<p>; Cylinder radius for dynamic reaction force groups (nm)</p>
<p>pull_r1 = 1</p>
<p>; Switch from r1 to r0 in case of dynamic reaction force</p>
<p>pull_r0 = 1.5</p>
<p>pull_constr_tol = 1e-06</p>
<p>pull_start = yes</p>
<p>pull_nstxout = 1</p>
<p>pull_nstfout = 1</p>
<p>; Number of pull groups </p>
<p>pull_ngroups = 1</p>
<p>; Group name, weight (default all 1), vector, init, rate (nm/ps), kJ/(mol*nm^2)</p>
<p>pull_group0 = C</p>
<p>pull_weights0 = </p>
<p>pull_pbcatom0 = 0</p>
<p>pull_group1 = H2O</p>
<p>pull_weights1 = </p>
<p>pull_pbcatom1 = 0</p>
<p>pull_vec1 = 0.0 0.0 1.0 </p>
<p>pull_init1 = 3.4</p>
<p>pull_rate1 = 0.02</p>
<p>pull_k1 = 837</p>
<p>pull_kB1 = 837</p>
<p>Is everything ok with pull_vec1, pull_init1, pull_rate1 (if I put 0 atoms will stay without any movement, but I suggest it will cause another result), pull (umbrella is harmonical, constrains - no) and pull_geometry (in the article was mentioned "distance" instead of "direction") ??? </p>
<p>I did experiments with different changes in parameters...Waiting for your comments. Thanks </p>
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