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<div style="color: rgb(49, 53, 59); font-family: 微软雅黑, Verdana, 'Microsoft Yahei', SimSun, sans-serif; line-height: 22.4px;">Hi,</div><div style="color: rgb(49, 53, 59); font-family: 微软雅黑, Verdana, 'Microsoft Yahei', SimSun, sans-serif; line-height: 22.4px;">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 =<span style="line-height: 22.4px;">direction-periodic</span>,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，how to calculate “distance at start”？</div><div style="color: rgb(49, 53, 59); font-family: 微软雅黑, Verdana, 'Microsoft Yahei', SimSun, sans-serif; line-height: 22.4px;">Thank you in advance.</div><div style="color: rgb(49, 53, 59); font-family: 微软雅黑, Verdana, 'Microsoft Yahei', SimSun, sans-serif; line-height: 22.4px;">My pull code is followed:</div><div><div><font color="#31353b" face="微软雅黑, Verdana, Microsoft Yahei, SimSun, sans-serif">; Pull code</font></div><div><font color="#31353b" face="微软雅黑, Verdana, Microsoft Yahei, SimSun, sans-serif">freezegrps = bot top</font></div><div><font color="#31353b" face="微软雅黑, Verdana, Microsoft Yahei, SimSun, sans-serif">freezedim = Y Y Y n y n</font></div><div><font color="#31353b" face="微软雅黑, Verdana, Microsoft Yahei, SimSun, sans-serif">pull = yes</font></div><div><font color="#31353b" face="微软雅黑, Verdana, Microsoft Yahei, SimSun, sans-serif">pull_ncoords = 2 ; two reaction coordinates x and z</font></div><div><font color="#31353b" face="微软雅黑, Verdana, Microsoft Yahei, SimSun, sans-serif">pull_ngroups = 2 ; one group defining one reaction coordinate</font></div><div><font color="#31353b" face="微软雅黑, Verdana, Microsoft Yahei, SimSun, sans-serif">pull_group1_name = top</font></div><div><font color="#31353b" face="微软雅黑, Verdana, Microsoft Yahei, SimSun, sans-serif">pull_group2_name = bot</font></div><div><font color="#31353b" face="微软雅黑, Verdana, Microsoft Yahei, SimSun, sans-serif">pull_coord1_type = umbrella ;harmonic potential</font></div><div><font color="#31353b" face="微软雅黑, Verdana, Microsoft Yahei, SimSun, sans-serif">pull_coord1_geometry= direction-periodic</font></div><div><font color="#31353b" face="微软雅黑, Verdana, Microsoft Yahei, SimSun, sans-serif">pull_coord1_vec = 1 0 0</font></div><div><font color="#31353b" face="微软雅黑, Verdana, Microsoft Yahei, SimSun, sans-serif">pull_coord1_origin = 0 0 0 </font></div><div><font color="#31353b" face="微软雅黑, Verdana, Microsoft Yahei, SimSun, sans-serif">pull_coord1_groups = 0 1</font></div><div><font color="#31353b" face="微软雅黑, Verdana, Microsoft Yahei, SimSun, sans-serif">pull_coord1_start = yes</font></div><div><font color="#31353b" face="微软雅黑, Verdana, Microsoft Yahei, SimSun, sans-serif">pull_coord1_k = 4000</font></div><div><font color="#31353b" face="微软雅黑, Verdana, Microsoft Yahei, SimSun, sans-serif">pull_coord1_rate = 0.005</font></div><div><font color="#31353b" face="微软雅黑, Verdana, Microsoft Yahei, SimSun, sans-serif"><br></font></div><div><font color="#31353b" face="微软雅黑, Verdana, Microsoft Yahei, SimSun, sans-serif">pull_coord2_type = constant-force</font></div><div><font color="#31353b" face="微软雅黑, Verdana, Microsoft Yahei, SimSun, sans-serif">pull_coord2_geometry= distance</font></div><div><font color="#31353b" face="微软雅黑, Verdana, Microsoft Yahei, SimSun, sans-serif">pull_coord2_dim = n n y</font></div><div><font color="#31353b" face="微软雅黑, Verdana, Microsoft Yahei, SimSun, sans-serif">pull_coord2_groups = 1 2</font></div><div><font color="#31353b" face="微软雅黑, Verdana, Microsoft Yahei, SimSun, sans-serif">pull_coord2_start = yes</font></div><div><font color="#31353b" face="微软雅黑, Verdana, Microsoft Yahei, SimSun, sans-serif">pull_coord2_k = 3838550 ;KJ mol^-1 nm^-1</font></div><div><font color="#31353b" face="微软雅黑, Verdana, Microsoft Yahei, SimSun, sans-serif"><br></font></div><div><font color="#31353b" face="微软雅黑, Verdana, Microsoft Yahei, SimSun, sans-serif">pull_group1_pbcatom = 5806</font></div><div><font color="#31353b" face="微软雅黑, Verdana, Microsoft Yahei, SimSun, sans-serif">;pull_group2_pbcatom = 1887</font></div><div><font color="#31353b" face="微软雅黑, Verdana, Microsoft Yahei, SimSun, sans-serif">pull-pbc-ref-prev-step-com = yes</font></div><div><font color="#31353b" face="微软雅黑, Verdana, Microsoft Yahei, SimSun, sans-serif"><br></font></div><div><font color="#31353b" face="微软雅黑, Verdana, Microsoft Yahei, SimSun, sans-serif"><br></font></div><div><font color="#31353b" face="微软雅黑, Verdana, Microsoft Yahei, SimSun, sans-serif"><br></font></div><div><font color="#31353b" face="微软雅黑, Verdana, Microsoft Yahei, SimSun, sans-serif">cos-acceleration = 0.05</font></div><div><font color="#31353b" face="微软雅黑, Verdana, Microsoft Yahei, SimSun, sans-serif">comm-mode = linear</font></div><div><font color="#31353b" face="微软雅黑, Verdana, Microsoft Yahei, SimSun, sans-serif">nstcomm = 10</font></div><div><font color="#31353b" face="微软雅黑, Verdana, Microsoft Yahei, SimSun, sans-serif">comm-grps =</font></div><div><font color="#31353b" face="微软雅黑, Verdana, Microsoft Yahei, SimSun, sans-serif"> </font></div></div><span>
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