<div>Dear all,</div>
<div> Thanks Florian and Justin for your suggestions</div>
<div> I am an beginner, so I am writing all the commands which I used</div>
<div> pdb2gmx -f *.pdb -o *.gro -p *.top</div>
<div>then</div>
<div>editconf -f *.gro -o *out.gro -c -d 0.8</div>
<div> </div>
<div>genbox -cp *out.gro -cs -o *b4ion.gro -p *.top</div>
<div> </div>
<div>grompp -f em.mdp -po *out.mdp -c *b4ion.gro -p *.top -o *b4ion.tpr</div>
<div> </div>
<div>neutralized system</div>
<div> </div>
<div>genion -s *b4ion.tpr -o *b4em.gro -pname Na -np 10 -g *ion.log</div>
<div> </div>
<div>select group 12</div>
<div> </div>
<div>editing in *.top file</div>
<div> </div>
<div>grompp -f em.mdp -c *b4em.gro -p *.top -o *em.tpr</div>
<div> </div>
<div>mdrun -s *em.tpr -o *em.trr -c *b4pr.gro -g em.log -e em.edr</div>
<div> </div>
<div>grompp -f pr.mdp -c *b4pr.gro -p *.top -o *pr.tpr</div>
<div> </div>
<div>mdrun -s *pr.tpr -o *pr.trr -c *b4md.gro -g pr.log -e pr.edr</div>
<div> </div>
<div>grompp -f md.mdp -c *b4md.gro -p *.top -o *md.tpr</div>
<div> </div>
<div>mdrun -s *md.tpr -o *md.trr -c *pmd.gro -g md.log -e md.edr</div>
<div> </div>
<div>HOPE this will help to understand my problem</div>
<div> </div>
<div> with regards</div>
<div> Anamika<br><br></div>