<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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