Hi all:<br> I want to pull three small molecules into a membrane along three vectors <span class="enfont">perpendicular to it</span> by constrainting<span class="enfont"></span>, the parameter setting is below:<br><span style="color: rgb(0, 102, 0);">pull = constraint</span><br style="color: rgb(0, 102, 0);">
<span style="color: rgb(0, 102, 0);">pull_constr_tol = 1e-5</span><br style="color: rgb(0, 102, 0);"><span style="color: rgb(0, 102, 0);">pull_geometry = position</span><br style="color: rgb(0, 102, 0);">
<span style="color: rgb(0, 102, 0);">pull_dim = Y Y Y</span><br style="color: rgb(0, 102, 0);"><span style="color: rgb(0, 102, 0);">pull_start = yes</span><br style="color: rgb(0, 102, 0);"><span style="color: rgb(0, 102, 0);">pull_nstxout = 50</span><br style="color: rgb(0, 102, 0);">
<span style="color: rgb(0, 102, 0);">pull_nstfout = 50</span><br style="color: rgb(0, 102, 0);"><span style="color: rgb(0, 102, 0);">pull_ngroups = 3</span><br style="color: rgb(0, 102, 0);"><span style="color: rgb(0, 102, 0);">pull_group0 = lipid ; reference group</span><br style="color: rgb(0, 102, 0);">
<span style="color: rgb(0, 102, 0);">pull_group1 = phe1 </span><br style="color: rgb(0, 102, 0);"><span style="color: rgb(0, 102, 0);">pull_vec1 = 0 0 -1 </span><br style="color: rgb(0, 102, 0);">
<span style="color: rgb(0, 102, 0);">pull_rate1 = 0.0002 ; [nm/ps] </span><br style="color: rgb(0, 102, 0);"><span style="color: rgb(0, 102, 0);">pull_group2 = phe2</span><br style="color: rgb(0, 102, 0);">
<span style="color: rgb(0, 102, 0);">pull_vec2 = 0 0 -1 </span><br style="color: rgb(0, 102, 0);"><span style="color: rgb(0, 102, 0);">pull_rate2 = 0.0002 ; [nm/ps] </span><br style="color: rgb(0, 102, 0);">
<span style="color: rgb(0, 102, 0);">pull_group3 = phe3 </span><br style="color: rgb(0, 102, 0);"><span style="color: rgb(0, 102, 0);">pull_vec3 = 0 0 -1 </span><br style="color: rgb(0, 102, 0);">
<span style="color: rgb(0, 102, 0);">pull_rate3 = 0.0002 ; [nm/ps] </span><br style="color: rgb(51, 255, 51);"><br> But I get an error :<br><br><span style="color: rgb(204, 0, 0);">Step 0, time 0 (ps) LINCS WARNING</span><br style="color: rgb(204, 0, 0);">
<span style="color: rgb(204, 0, 0);">relative constraint deviation after LINCS:</span><br style="color: rgb(204, 0, 0);"><span style="color: rgb(204, 0, 0);">rms 2465.976683, max 48465.484375 (between atoms 8716 and 8715)</span><br style="color: rgb(204, 0, 0);">
<span style="color: rgb(204, 0, 0);">bonds that rotated more than 30 degrees:</span><br style="color: rgb(204, 0, 0);"><span style="color: rgb(204, 0, 0);"> atom 1 atom 2 angle previous, current, constraint length</span><br style="color: rgb(204, 0, 0);">
<span style="color: rgb(204, 0, 0);"> 8777 8776 82.5 0.1470 123.6644 0.1470</span><br style="color: rgb(204, 0, 0);"><span style="color: rgb(204, 0, 0);"> 8775 8776 97.3 0.1530 1185.9658 0.1530</span><br style="color: rgb(204, 0, 0);">
<span style="color: rgb(204, 0, 0);"> 8774 8775 66.1 0.1530 1091.0201 0.1530</span><br style="color: rgb(204, 0, 0);"><span style="color: rgb(204, 0, 0);"> 8773 8774 96.5 0.1390 11850.9688 0.1390</span><br style="color: rgb(204, 0, 0);">
<span style="color: rgb(204, 0, 0);"> 8771 8773 81.2 0.1390 22400.8809 0.1390</span><br style="color: rgb(204, 0, 0);"><span style="color: rgb(204, 0, 0);"> 8771 8772 92.8 0.1890 19976.3652 0.1890</span><br style="color: rgb(204, 0, 0);">
<span style="color: rgb(204, 0, 0);"> 8770 8771 93.0 0.1390 22574.0859 0.1390</span><br style="color: rgb(204, 0, 0);"><span style="color: rgb(204, 0, 0);"> 8769 8774 41.7 0.1390 866.0833 0.1390</span><br style="color: rgb(204, 0, 0);">
<span style="color: rgb(204, 0, 0);"> 8768 8769 160.1 0.1390 693.7319 0.1390</span><br style="color: rgb(204, 0, 0);"><span style="color: rgb(204, 0, 0);"> 8768 8770 79.8 0.1390 4601.1436 0.1390</span><br style="color: rgb(204, 0, 0);">
<span style="color: rgb(204, 0, 0);"> 8767 8768 99.9 0.1431 1037.8502 0.1430</span><br style="color: rgb(204, 0, 0);"><span style="color: rgb(204, 0, 0);"> 8780 8777 109.1 0.1000 20.7450 0.1000</span><br style="color: rgb(204, 0, 0);">
<span style="color: rgb(204, 0, 0);"> 8779 8777 118.4 0.1000 20.6520 0.1000</span><br style="color: rgb(204, 0, 0);"><span style="color: rgb(204, 0, 0);"> 8778 8777 107.8 0.1000 21.5070 0.1000</span><br style="color: rgb(204, 0, 0);">
<span style="color: rgb(204, 0, 0);"> 8746 8745 81.2 0</span><br style="color: rgb(204, 0, 0);"><span style="color: rgb(204, 0, 0);">...</span><br style="color: rgb(204, 0, 0);"><span style="color: rgb(204, 0, 0);">Wrote pdb files with previous and current coordinates</span><br style="color: rgb(204, 0, 0);">
<span style="color: rgb(204, 0, 0);">step 0</span><br style="color: rgb(204, 0, 0);"><span style="color: rgb(204, 0, 0);">rank 5 in job 1 c0201_60409 caused collective abort of all ranks</span><br style="color: rgb(204, 0, 0);">
<span style="color: rgb(204, 0, 0);"> exit status of rank 5: killed by signal 11 </span><br style="color: rgb(204, 0, 0);"><span style="color: rgb(204, 0, 0);">rank 3 in job 1 c0201_60409 caused collective abort of all ranks</span><br style="color: rgb(204, 0, 0);">
<span style="color: rgb(204, 0, 0);"> exit status of rank 3: killed by signal 11 </span><br style="color: rgb(204, 0, 0);"><span style="color: rgb(204, 0, 0);">rank 1 in job 1 c0201_60409 caused collective abort of all ranks</span><br style="color: rgb(204, 0, 0);">
<span style="color: rgb(204, 0, 0);"> exit status of rank 1: killed by signal 11 </span><br style="color: rgb(204, 0, 0);"><br><br>I don't know where is the error coming from? I test the same system by umbrella pulling, it works well with the parameter as below:<br>
; COM PULLING <br>; Pull type: no, umbrella, constraint or constant_force<br>pull = umbrella<br>; Pull geometry: distance, direction, cylinder or position<br>pull_geometry = position<br>
; Select components for the pull vector. default: Y Y Y<br>pull_dim = Y Y Y<br>; Cylinder radius for dynamic reaction force groups (nm)<br>pull_r1 = 1<br>; Switch from r1 to r0 in case of dynamic reaction force<br>
pull_r0 = 1.5<br>pull_constr_tol = 1e-06<br>pull_start = yes<br>pull_nstxout = 50<br>pull_nstfout = 50<br>; Number of pull groups <br>pull_ngroups = 3<br>
; Group name, weight (default all 1), vector, init, rate (nm/ps), kJ/(mol*nm^2)<br>pull_group0 = lipid<br>pull_weights0 = <br>pull_pbcatom0 = 0<br>pull_group1 = phe1<br>pull_weights1 = <br>
pull_pbcatom1 = 0<br>pull_vec1 = 0 0 -1<br>pull_init1 = 0.0 0.0 0.0<br>pull_rate1 = 0.00005<br>pull_k1 = 500<br><br>pull_group2 = phe2<br>
pull_weights2 = <br>pull_pbcatom2 = 0<br>pull_vec2 = 0 0 1<br>pull_init2 = 0.0 0.0 0.0<br>pull_rate2 = 0.00005<br>pull_k2 = 500<br><br>pull_group3 = phe3<br>
pull_weights3 = <br>pull_pbcatom3 = 0<br>pull_vec3 = 0 0 1<br>pull_init3 = 0.0 0.0 0.0<br>pull_rate3 = 0.00002<br>pull_k3 = 500<br><br><br>
<br><br><br><br>