Hello!
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
Thanks
Varun