EM chaning peptide coordinated even after using position restrain

I am tring to see CPP simulation across lipid bilayer.


After energy minimization, my peptide coordinate are changing and peptide crossed the membrane and reach to other side…I am using position restrain but it is not working… Can someone suggest what I am doing wrong here?

gmx pdb2gmx -f seq1.X.pdb -o seq1.X.gro -ignh -ter -water spc (14, 1, 1)

gmx grompp -f minim.mdp -c dppc128.pdb -p topol_dppc.top -maxwarn 1 -o dppc.tpr

gmx trjconv -s dppc.tpr -f dppc128.pdb -o dppc128_whole.gro -pbc mol -ur compact

gmx editconf -f seq1.X.gro -o seq1.X-newbox.gro -center 3.280 3.281 7.5965 -box 6.41840 6.44350 6.59650

cat seq1.X-newbox.gro dppc128_whole.gro > system.gro — corrected topol.top – add DPPC 128, dppc.itp and strong_posre.itp

gmx genrestr -f seq1.X-newbox.gro -o strong_posre.itp -fc 1000 1000 1000

gmx solvate -cp system.gro -cs spc216.gro -o system_solv.gro -p topol.top – fixed water molecule in topol.top 5409

gmx grompp -f ions.mdp -c system_solv.gro -p topol.top -maxwarn 1 -o ions.tpr

gmx genion -s ions.tpr -o solv_ions.gro -p topol.top -pname NA -nname CL -neutral #selected 15

gmx grompp -f minim.mdp -c solv_ions.gro -p topol.top -r solv_ions.gro -maxwarn 1 -o em.tpr (used protein restrain in mdp)

gmx mdrun -v -deffnm em



The issue isn’t anything at all related to restraints. Your box isn’t large enough to contain the system, so the protein is simply jumping across a periodic boundary (but it’s also interacting with itself). Look at this:

You’re defining a box that is 6.59650 along the z-axis but trying to center the system at 7.5965 nm along z. You’re centering it “outside” of the central unit cell. You need a larger box that sensibly fits the contents of the system.

It worked. Thank you so much for your help.