<div>Hello everyone,</div>
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<div>I use the g_order to get the order parameter of the tails( C1A, C2A, C3A, C4A) of DPPC. The are 100 molecules of DPPC</div>
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<div>1. I use the make_ndx -f dppc.trr -n index to produce the index file.</div>
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<div>> a C1A</div>
<div>> a C2A</div>
<div>> a C3A</div>
<div>> a C4A</div>
<div>> del 0-3</div>
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<div><font color="#ff0000">Q_1: Is the method right to produce the index file? </font></div>
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<div>Then there only four groups orderly named C1A, C2A, C3A, C4A in the index file.</div>
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<div>2. I use the g_order -n index -s npt.tpr ... to get the order parameter. However, there are lots of errors</div>
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<div>.........</div>
<div>WARNING: distance between atoms 29777 and 29779 > 0.3 nm (0.897513). Index file might be corrupt.<br>WARNING: distance between atoms 29789 and 29791 > 0.3 nm (0.709495). Index file might be corrupt.<br>WARNING: distance between atoms 29801 and 29803 > 0.3 nm (0.692954). Index file might be corrupt.<br>
WARNING: distance between atoms 29813 and 29815 > 0.3 nm (0.784918). Index file might be corrupt.<br>WARNING: distance between atoms 29825 and 29827 > 0.3 nm (0.839048). Index file might be corrupt.<br>WARNING: distance between atoms 29837 and 29839 > 0.3 nm (0.851105). Index file might be corrupt.<br>
WARNING: distance between atoms 29849 and 29851 > 0.3 nm (0.790752). Index file might be corrupt.<br>WARNING: distance between atoms 29861 and 29863 > 0.3 nm (0.836583). Index file might be corrupt.<br>WARNING: distance between atoms 29873 and 29875 > 0.3 nm (0.854105). Index file might be corrupt.<br>
WARNING: distance between atoms 29885 and 29887 > 0.3 nm (0.847901). Index file might be corrupt.<br>WARNING: distance between atoms 29897 and 29899 > 0.3 nm (0.758556). Index file might be corrupt.<br>...........</div>
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<div><font color="#ff0000">Why?</font></div>
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<div>3. Result</div>
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<div>Last frame 4 time 240.000 </div>
<div>Read trajectory. Printing parameters to file<br>Atom 1 Tensor: x=-0.267416 , y=-0.245994, z=0.51341<br>Atom 2 Tensor: x=-0.207203 , y=-0.171233, z=0.378436</div>
<div>Back Off! I just backed up order.xvg to ./#order.xvg.1#</div>
<div>Back Off! I just backed up deuter.xvg to ./#deuter.xvg.1#</div>
<div>gcq#51: "The Stingrays Must Be Fat This Year" (Red Hot Chili Peppers)</div>
<div>[tianwd@localhost dppcden5]$ cat order.xvg <br># This file was created Sun Apr 23 10:10:35 2006<br># by the following command:<br># g_order -f traj.trr -n index.ndx -s npt.tpr -o -e 240 <br>#<br># g_order is part of G R O M A C S:<br>
#<br># Gallium Rubidium Oxygen Manganese Argon Carbon Silicon<br>#<br>@ title "Order tensor diagonal elements"<br>@ xaxis label "Atom"<br>@ yaxis label "S"<br>@TYPE xy<br> 1 -0.267416 -0.245994 0.51341<br>
2 -0.207203 -0.171233 0.378436<br>[tianwd@localhost dppcden5]$ <br><br clear="all"><br>-- <br>wende<br></div>