[gmx-users] Re: gmx-users Digest, Vol 102, Issue 112

Ali Alizadeh ali.alizadehmojarad at gmail.com
Thu Oct 18 12:45:56 CEST 2012

Dear Justin

Please check my commands, Are these correct, step by step?

If these are correct then i will start my simulation with longer time,

1- pdb2gmx -f mixture.pdb -o mix -p mix

2- editconf -f mix.gro -o mix2.pdb   ; for obtain a clean .pdb for
obtaining clean .gro and clean .top

3- pdb2gmx -f mix2.pdb -o mix2.gro -p mix2.top

   STEP 1 :  EM

5- grompp -f minim.mdp -c mix2.gro -p mix2.top -o em.tpr

6- mdrun -v -deffnm em


7- editconf -f em.gro -o em.pdb   ; to earn em.gro and em.top for next NPT EM

8- pdb2gmx -f em.pdb -o nvt -p nvt

9- grompp -f nvt.mdp -c nvt.gro -p nvt.top -o nvt.tpr

10- mdrun -v -deffnm nvt

11- g_energy -f nvt.edr

12- xmgrace  energy.xvg


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