<div dir="ltr"><p style="MARGIN: 0in 0in 0pt" class="MsoNormal"><font size="3"><span style="FONT-FAMILY: 'Calibri','sans-serif'; COLOR: #1f497d">H</span><span style="FONT-FAMILY: 'Calibri','sans-serif'">i,</span></font></p>
<p style="MARGIN: 0in 0in 0pt" class="MsoNormal"><span style="FONT-FAMILY: 'Calibri','sans-serif'"><font size="3"> </font></span></p>
<p style="MARGIN: 0in 0in 0pt" class="MsoNormal"><span style="FONT-FAMILY: 'Calibri','sans-serif'"><font size="3">I am running a simulation on the complex 1aik.pdb in 310K. I wanted to see if the complex is seeing its next periodic image, so I used the g_mindist command with the -pi option. My command line was:</font></span></p>
<p style="MARGIN: 0in 0in 0pt" class="MsoNormal"><span style="FONT-FAMILY: 'Calibri','sans-serif'"><font size="3">g_mindist -f run.xtc -s run.gro -n index.ndx -od tmp.xvg -pi </font></span></p>
<p style="MARGIN: 0in 0in 0pt" class="MsoNormal"><span style="FONT-FAMILY: 'Calibri','sans-serif'"><font size="3">The output (see below) was stable until ~344ps when there is a jump in the max internal distance (third column) from ~6nm to ~22nm. After the jump the numbers are reduced back to ~6nm and remained stable until the run is completed at 1ns.</font></span></p>
<p style="MARGIN: 0in 0in 0pt" class="MsoNormal"><span style="FONT-FAMILY: 'Calibri','sans-serif'"><font size="3">Does anyone know how to explain this jump? Is this a real problem or just a visualization artifact? Is there a way to avoid such jumps?</font></span></p>
<p style="MARGIN: 0in 0in 0pt" class="MsoNormal"><span style="FONT-FAMILY: 'Calibri','sans-serif'"><font size="3"> </font></span></p>
<p style="MARGIN: 0in 0in 0pt" class="MsoNormal"><span style="FONT-FAMILY: 'Calibri','sans-serif'"><font size="3">Here is the mdp file I used:</font></span></p>
<p style="MARGIN: 0in 0in 0pt" class="MsoNormal"><span style="FONT-FAMILY: 'Calibri','sans-serif'"><font size="3">------run.mdp------</font></span></p>
<p style="MARGIN: 0in 0in 0pt" class="MsoNormal"><span style="FONT-FAMILY: 'Calibri','sans-serif'"><font size="3">integrator = md</font></span></p>
<p style="MARGIN: 0in 0in 0pt" class="MsoNormal"><span style="FONT-FAMILY: 'Calibri','sans-serif'"><font size="3">nsteps = 1000000</font></span></p>
<p style="MARGIN: 0in 0in 0pt" class="MsoNormal"><span style="FONT-FAMILY: 'Calibri','sans-serif'"><font size="3">dt = 0.001</font></span></p>
<p style="MARGIN: 0in 0in 0pt" class="MsoNormal"><span style="FONT-FAMILY: 'Calibri','sans-serif'"><font size="3">coulombtype = pme</font></span></p>
<p style="MARGIN: 0in 0in 0pt" class="MsoNormal"><span style="FONT-FAMILY: 'Calibri','sans-serif'"><font size="3">vdw-type = cut-off</font></span></p>
<p style="MARGIN: 0in 0in 0pt" class="MsoNormal"><span style="FONT-FAMILY: 'Calibri','sans-serif'"><font size="3">tcoupl = Berendsen</font></span></p>
<p style="MARGIN: 0in 0in 0pt" class="MsoNormal"><span style="FONT-FAMILY: 'Calibri','sans-serif'"><font size="3">tc-grps = protein non-protein</font></span></p>
<p style="MARGIN: 0in 0in 0pt" class="MsoNormal"><span style="FONT-FAMILY: 'Calibri','sans-serif'"><font size="3">tau-t = 0.1 0.1</font></span></p>
<p style="MARGIN: 0in 0in 0pt" class="MsoNormal"><span style="FONT-FAMILY: 'Calibri','sans-serif'"><font size="3">ref-t = 310 310</font></span></p>
<p style="MARGIN: 0in 0in 0pt" class="MsoNormal"><span style="FONT-FAMILY: 'Calibri','sans-serif'"><font size="3">nstxout = 100</font></span></p>
<p style="MARGIN: 0in 0in 0pt" class="MsoNormal"><span style="FONT-FAMILY: 'Calibri','sans-serif'"><font size="3">nstvout = 0</font></span></p>
<p style="MARGIN: 0in 0in 0pt" class="MsoNormal"><span style="FONT-FAMILY: 'Calibri','sans-serif'"><font size="3">nstxtcout = 100</font></span></p>
<p style="MARGIN: 0in 0in 0pt" class="MsoNormal"><span style="FONT-FAMILY: 'Calibri','sans-serif'"><font size="3">nstenergy = 100</font></span></p>
<p style="MARGIN: 0in 0in 0pt" class="MsoNormal"><span style="FONT-FAMILY: 'Calibri','sans-serif'"><font size="3">comm_mode = Linear ; Angular</font></span></p>
<p style="MARGIN: 0in 0in 0pt" class="MsoNormal"><span style="FONT-FAMILY: 'Calibri','sans-serif'"><font size="3">comm_grps = Protein</font></span></p>
<p style="MARGIN: 0in 0in 0pt" class="MsoNormal"><span style="FONT-FAMILY: 'Calibri','sans-serif'"><font size="3">xtc_grps = Protein</font></span></p>
<p style="MARGIN: 0in 0in 0pt" class="MsoNormal"><span style="FONT-FAMILY: 'Calibri','sans-serif'"><font size="3">energygrps = Protein</font></span></p>
<p style="MARGIN: 0in 0in 0pt" class="MsoNormal"><span style="FONT-FAMILY: 'Calibri','sans-serif'"><font size="3">------------------</font></span></p>
<p style="MARGIN: 0in 0in 0pt" class="MsoNormal"><span style="FONT-FAMILY: 'Calibri','sans-serif'"><font size="3"> </font></span></p>
<p style="MARGIN: 0in 0in 0pt" class="MsoNormal"><span style="FONT-FAMILY: 'Calibri','sans-serif'"><font size="3">Thanks,</font></span></p>
<p style="MARGIN: 0in 0in 0pt" class="MsoNormal"><span style="FONT-FAMILY: 'Calibri','sans-serif'"><font size="3">Ifat</font></span></p>
<p style="MARGIN: 0in 0in 0pt" class="MsoNormal"><span style="FONT-FAMILY: 'Calibri','sans-serif'"><font size="3"> </font></span></p>
<p style="MARGIN: 0in 0in 0pt" class="MsoNormal"><span style="FONT-FAMILY: 'Calibri','sans-serif'"><font size="3">The output:</font></span></p>
<p style="MARGIN: 0in 0in 0pt" class="MsoNormal"><font size="3" face="Times New Roman">343.7 10.813 5.924 16.445 16.445 16.445</font></p>
<p style="MARGIN: 0in 0in 0pt" class="MsoNormal"><font size="3" face="Times New Roman">343.8 10.809 5.949 16.445 16.445 16.445</font></p>
<p style="MARGIN: 0in 0in 0pt" class="MsoNormal"><font size="3" face="Times New Roman">343.9 10.804 5.959 16.445 16.445 16.445</font></p>
<p style="MARGIN: 0in 0in 0pt" class="MsoNormal"><font size="3" face="Times New Roman">344 10.808 5.974 16.445 16.445 16.445</font></p>
<p style="MARGIN: 0in 0in 0pt" class="MsoNormal"><font size="3" face="Times New Roman">344.1 0.18 21.982 16.445 16.445 16.445</font></p>
<p style="MARGIN: 0in 0in 0pt" class="MsoNormal"><font size="3" face="Times New Roman">344.2 10.778 5.977 16.445 16.445 16.445</font></p>
<p style="MARGIN: 0in 0in 0pt" class="MsoNormal"><font size="3" face="Times New Roman">344.3 10.768 5.996 16.445 16.445 16.445</font></p>
<p style="MARGIN: 0in 0in 0pt" class="MsoNormal"><font size="3" face="Times New Roman">344.4 10.764 6.016 16.445 16.445 16.445</font></p>
<p style="MARGIN: 0in 0in 0pt" class="MsoNormal"><font size="3" face="Times New Roman">344.5 10.722 6.029 16.445 16.445 16.445</font></p>
<p style="MARGIN: 0in 0in 0pt" class="MsoNormal"><font size="3" face="Times New Roman">344.6 10.774 6.01 16.445 16.445 16.445</font></p>
<p style="MARGIN: 0in 0in 0pt" class="MsoNormal"><font size="3" face="Times New Roman">344.7 0.174 21.984 16.445 16.445 16.445</font></p>
<p style="MARGIN: 0in 0in 0pt" class="MsoNormal"><font size="3" face="Times New Roman">344.8 0.176 21.98 16.445 16.445 16.445</font></p>
<p style="MARGIN: 0in 0in 0pt" class="MsoNormal"><font size="3" face="Times New Roman">344.9 0.17 22.002 16.445 16.445 16.445</font></p>
<p style="MARGIN: 0in 0in 0pt" class="MsoNormal"><font size="3" face="Times New Roman">345 0.173 21.981 16.445 16.445 16.445</font></p>
<p style="MARGIN: 0in 0in 0pt" class="MsoNormal"><font size="3" face="Times New Roman">345.1 0.191 21.954 16.445 16.445 16.445</font></p>
<p style="MARGIN: 0in 0in 0pt" class="MsoNormal"><font size="3" face="Times New Roman">345.2 0.183 21.958 16.445 16.445 16.445</font></p>
<p style="MARGIN: 0in 0in 0pt" class="MsoNormal"><font size="3" face="Times New Roman">345.3 0.181 22.012 16.445 16.445 16.445</font></p>
<p style="MARGIN: 0in 0in 0pt" class="MsoNormal"><font size="3" face="Times New Roman">345.4 0.17 22.054 16.445 16.445 16.445</font></p>
<p style="MARGIN: 0in 0in 0pt" class="MsoNormal"><font size="3" face="Times New Roman">345.5 0.168 22.054 16.445 16.445 16.445</font></p>
<p style="MARGIN: 0in 0in 0pt" class="MsoNormal"><font size="3" face="Times New Roman">345.6 0.189 22.039 16.445 16.445 16.445</font></p>
<p style="MARGIN: 0in 0in 0pt" class="MsoNormal"><font size="3" face="Times New Roman">345.7 0.171 22.007 16.445 16.445 16.445</font></p>
<p style="MARGIN: 0in 0in 0pt" class="MsoNormal"><font size="3" face="Times New Roman">345.8 0.186 22.031 16.445 16.445 16.445</font></p>
<p style="MARGIN: 0in 0in 0pt" class="MsoNormal"><font size="3" face="Times New Roman">345.9 0.171 22.077 16.445 16.445 16.445</font></p>
<p style="MARGIN: 0in 0in 0pt" class="MsoNormal"><font size="3" face="Times New Roman">346 0.187 21.99 16.445 16.445 16.445</font></p>
<p style="MARGIN: 0in 0in 0pt" class="MsoNormal"><font size="3" face="Times New Roman">346.1 0.173 21.984 16.445 16.445 16.445</font></p>
<p style="MARGIN: 0in 0in 0pt" class="MsoNormal"><font size="3" face="Times New Roman">346.2 0.181 22.02 16.445 16.445 16.445</font></p>
<p style="MARGIN: 0in 0in 0pt" class="MsoNormal"><font size="3" face="Times New Roman">346.3 10.82 5.984 16.445 16.445 16.445</font></p>
<p style="MARGIN: 0in 0in 0pt" class="MsoNormal"><font size="3" face="Times New Roman">346.4 10.81 6.002 16.445 16.445 16.445</font></p>
<p style="MARGIN: 0in 0in 0pt" class="MsoNormal"><font size="3" face="Times New Roman">346.5 10.819 6.008 16.445 16.445 16.445</font></p>
<p style="MARGIN: 0in 0in 0pt" class="MsoNormal"><font size="3" face="Times New Roman">346.6 10.813 5.996 16.445 16.445 16.445</font></p>
<p style="MARGIN: 0in 0in 0pt" class="MsoNormal"><font size="3" face="Times New Roman">346.7 10.781 6.006 16.445 16.445 16.445</font></p>
<p style="MARGIN: 0in 0in 0pt" class="MsoNormal"><font size="3" face="Times New Roman">346.8 10.793 6.026 16.445 16.445 16.445</font></p>
<p style="MARGIN: 0in 0in 0pt" class="MsoNormal"><font size="3" face="Times New Roman">346.9 10.745 5.985 16.445 16.445 16.445</font></p>
<p style="MARGIN: 0in 0in 0pt" class="MsoNormal"><font size="3" face="Times New Roman">347 10.762 5.999 16.445 16.445 16.445</font></p>
<p style="MARGIN: 0in 0in 0pt" class="MsoNormal"><font size="3" face="Times New Roman">347.1 10.781 5.984 16.445 16.445 16.445</font></p>
<p style="MARGIN: 0in 0in 0pt" class="MsoNormal"><font size="3" face="Times New Roman">347.2 10.784 6.002 16.445 16.445 16.445</font></p>
<p style="MARGIN: 0in 0in 0pt" class="MsoNormal"><span style="FONT-FAMILY: 'Calibri','sans-serif'; FONT-SIZE: 11pt"> </span></p>
<p style="MARGIN: 0in 0in 0pt" class="MsoNormal"><font size="3" face="Times New Roman"> </font></p></div>