[gmx-users] Abnormal RMSD

Anamika Awasthi aawasthi28 at gmail.com
Fri Feb 15 17:23:17 CET 2008

Dear all,
     Thanks Florian and Justin for your suggestions
      I am an beginner, so I am writing all the commands which I used
 pdb2gmx -f *.pdb -o *.gro -p *.top
editconf -f *.gro -o *out.gro -c -d 0.8

genbox -cp *out.gro -cs -o *b4ion.gro -p *.top

grompp -f em.mdp -po *out.mdp -c *b4ion.gro -p *.top -o *b4ion.tpr

neutralized system

genion -s *b4ion.tpr -o *b4em.gro -pname Na -np 10 -g *ion.log

select group 12

editing in *.top file

grompp -f em.mdp -c *b4em.gro -p *.top -o *em.tpr

mdrun -s *em.tpr -o *em.trr -c *b4pr.gro -g em.log -e em.edr

grompp -f pr.mdp -c *b4pr.gro -p *.top -o *pr.tpr

mdrun -s *pr.tpr -o *pr.trr -c *b4md.gro -g pr.log -e pr.edr

grompp -f md.mdp -c *b4md.gro -p *.top -o *md.tpr

mdrun -s *md.tpr -o *md.trr -c *pmd.gro -g md.log -e md.edr

HOPE this will help to understand my problem

 with regards
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