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<span>Hi,</span></div><div>There are two groups in my system.When I use the pull code to pull one group along the axis X, setting pull_coord1_geometry =direction,I am confused with the "distance at start" and the "reference at t=0".Could anyone can tell me how to understand these?And if I use the absolute reference,how to understand these? For example,when I set the pull_coord1_origin=0 0 0,what means the "distance at start"?</div><div>Thank you in advance.</div><div>My pull code is followed:</div><div><span style="line-height: 1.6;">; Pull code</span></div><div><div>freezegrps = bot top</div><div>freezedim = Y Y Y N N N</div><div>pull = yes</div><div>pull_ncoords = 1 ; only one reaction coordinate</div><div>pull_ngroups = 2 ; one group defining one reaction coordinate</div><div>pull_group1_name = top</div><div>pull_group2_name = bot</div><div>pull_coord1_type = constant-force</div><div>pull_coord1_geometry= direction</div><div>;pull_coord1_origin =</div><div>pull_coord1_vec = 1 0 0</div><div>pull_coord1_groups = 1 2</div><div>pull_coord1_start = yes</div><div>;pull_coord1_rate = -0.0001</div><div>pull_coord1_dim = y n n</div><div>pull_coord1_k = 5000 ;KJ mol^-1 nm^-1 </div><div>cos-acceleration = 0.05</div><div>pull_group1_pbcatom = 1384</div><div>pull_group2_pbcatom = 554</div><div>comm-mode = linear</div><div>nstcomm = 10</div><div>aomm-grps =</div></div><div><br></div><div>
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