- Add Box Coordinates to Coordinate File
editconf_d -bt cubic -c -f 1.gro -o 1_box.gro -d 1.2
- Solvate Created Box using AMBER TIP3 Water
genbox_d -cp 1_box.gro -cs ffamber_tip3p.gro -o 1_box_em.gro -p UDPGlcNAc_new.top
- Prepare Generic Input File for Energy Minimization (Water only)
grompp_d -f ../em.mdp -c 1_box_em.gro -p UDPGlcNAc_new.top -o 1_em.tpr
- Add Ion
genion_d -s 1_em.tpr -o 1_ion.gro -pname Mg -pq 2 -np 1 -g log
- Reposition Ion
../scripts/ionPlacement.pl 1_ion.gro 35 > 1_ion_repl.gro
- Prepare Generic Input File for Energy Minimization (Ion Added)
grompp_d -f ../em_ion.mdp -c 1_ion.gro -p UDPGlcNAc_new_ion.top-o 1_ion.tpr
- Run Energy Minimization for Ion File
mdrun_d -s 1_ion.tpr -o 1_ion.trr -c 1_ion_min.gro
- Prepare Generic Input File For Production Run Ion
grompp_d -f ../run.mdp -c 1_ion_min.gro -p UDPGlcNAc_new_ion.top -o ion_run.tpr
- Start Production Simulation of Ion File (including equilibration phase)
mdrun_d -v -s ion_run.tpr -o 1_ion_run.trr -c run.gro
- Start Production Simulation of Water File (including equilibration phase)
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