Dear users,<br><br>I am a beginner with gromacs. I converted a sample pdb file to gromacs file using "pdb2gmx" and then converted it back to pdb file using "genconf" but I found that positions of atoms was changed and so was their thermal factor. I did not understand why there was change in position of the atoms. when I observed both of them using pymol I found inconsistency in type of atoms and bond locations.<br>
<br>can you please explain why this happened .<br><br>thank you,<br><br>Harshith <br><br> <br>