<div>Dear Mark</div>
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<div><strong>(1)</strong> I did following steps for obtaining superimposed structure:</div>
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<div>I obtained 0.gro and 5000.gro files by above command                  <br>                                                                      <br>trjconv -f *.xtc -s *.tpr -o n.gro -dump n-1                          <br>
                                                                      <br>I concatenated 2 input files ( 0.gro and 5000.gro).                   <br>                                                                      <br>
trjcat -f 0.gro 5000.gro -o f.xtc                                    <br>                                                                      <br>finally,                                                              <br>
                                                                      <br>trjconv -f f.xtc -s *.gro  -o f.pdb -ter -fit progressive -n n.ndx </div>
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<div>simulation time was 5000 ps.</div>
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<div><strong>(2)</strong> I used command : [g_confrms -f1 initial.gro  -f2 final.gro -n1 1.ndx -n2 2.ndx -o fit.pdb -fit] </div>
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<div>to obtain superimposed structure of initial and final structures. I saw fit.pdb file by vmd but fit.pdb obtained was very mixed,busy and unclear.<br><br>is my manner true? </div>
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<div>which of manner mentioned above is true?</div>
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