[gmx-users] calculate potential in the box contain ions

[Saeid Akbarshahi]

Dear users


The simulation box contains sodium and chloride ions

start simulation

pdb2gmx -f ion.pdb -posrefc 0

Force Field : AMBER99SB-ILDN  - Water TIP3P


editconf -f conf.gro -bt cubic -box 3 3 3

genbox -cp out.gro -cs spc216.gro -o 5.gro -p topol.top

grompp -f minim.mdp -c 5.gro -p topol.top

mdrun -s topol.tpr

grompp -f nvt.mdp -c confout.gro -p topol.top -o md.tpr

mdrun -s md.tpr

Whether the simulation and results iscorrect ?
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