Molecular-Dynamics-Materials

MD-Step

gmx grompp -f step6.0_minimization.mdp -c 4194_PIP30.gro -r step5_input.gro -p topol.top -o em.tpr

gmx mdrun -deffnm em

gmx grompp -f step6.1_equilibration.mdp -c em.gro -r em.gro -p topol.top -o eq1.tpr -n index.ndx

gmx mdrun -deffnm eq1

gmx grompp -f step6.2_equilibration.mdp -c eq1.gro -r eq1.gro -p topol.top -o eq2.tpr -n index.ndx

gmx mdrun -deffnm eq2

gmx grompp -f step6.3_equilibration.mdp -c eq2.gro -r eq2.gro -p topol.top -o eq3.tpr -n index.ndx

gmx mdrun -deffnm eq3

gmx grompp -f step6.4_equilibration.mdp -c eq3.gro -r eq3.gro -p topol.top -o eq4.tpr -n index.ndx

gmx mdrun -deffnm eq4

gmx grompp -f step6.5_equilibration.mdp -c eq4.gro -r eq4.gro -p topol.top -o eq5.tpr -n index.ndx

gmx mdrun -deffnm eq5

gmx grompp -f step6.6_equilibration.mdp -c eq5.gro -r eq5.gro -p topol.top -o eq6.tpr -n index.ndx

gmx mdrun -deffnm eq6

gmx grompp -f step7_production.mdp -o md.tpr -c eq6.gro -p topol.top -n index.ndx

nohup gmx mdrun -deffnm md -pme gpu -nb gpu -bonded gpu -v &

if interrupted,

nohup gmx mdrun -s md.tpr -cpi md.cpt -deffnm md -nb gpu -v &

MD-Analyze

gmx make_ndx -f md.gro -o prolig_center.ndx

3 groups: pro_lig lipid pro_lig_lipid

check groups : gmx make_ndx -f md.gro -n prolig_center.ndx

gmx trjconv -s md.tpr -f md.trr -o noPBC_step1.trr -pbc mol -center -n prolig_center.ndx

select pro_lig_lipid and when you want to output all the atoms in this system, just select system at the secondary selection)

RMSD

gmx rms -f noPBC_step1.trr -s md.tpr -o md-rmsd.xvg -n prolig_center.ndx

select Backbone group twice.

extract stable scale following RMSD analysis

gmx trjconv -f noPBC_step1.trr -b 250000 -e 500000 -o analyze.xtc

RMSF

gmx rmsf -f analyze.xtc -s md.tpr -o rmsf.xvg -res -n prolig_center.ndx

select Backbone group.

Rg

gmx gyrate -s md.tpr -f noPBC_step1.trr -o md-gyrate.xvg -n prolig_center.ndx

select Backbone group.

SASA

gmx sasa -f noPBC_step1.trr -s md.tpr -o md-area.xvg -n prolig_center.ndx

select Backbone group.

H Bonds

gmx hbond -f noPBC_step1.trr -s md.tpr -n prolig_center.ndx -num hbnum.xvg -hbn hbonds.ndx -hbm hbmap.xpm

select 1 Protein and 13 UNK

PCA

gmx rms -s md.tpr -f noPBC_step1.trr -o FEL_rmsd.xvg -n prolig_center.ndx

gmx gyrate -s md.tpr -f noPBC_step1.trr -o FEL_gyrate.xvg -n prolig_center.ndx

pc_combine.py FEL_rmsd.xvg FEL_gyrate.xvg output.xvg (3 lines in order: time, rmsd, rg)

gmx sham -tsham 310 -nlevels 100 -f output.xvg -ls gibbs.xpm -g gibbs.log -lsh enthalpy.xpm -lss entropy.xpm

python xpm2png.py -ip yes -f gibbs.xpm (sources/xpm_show/xpm2png.py)

_check bindex.ndx and gibbs.log to find mini-energy-conformation

To check the trr: gmx check -f noPBC_step1.trr_

gmx trjconv -s md.tpr -f prolig_fit.xtc -o 4194.pdb -sep -b 4100 -e 4100 -pbc mol -n prolig_center.ndx

extract the best mini-conformation into next new cycles until 3 times at least.

MM/PBSA

gmx trjconv -f noPBC_step1.trr -b 490000 -e 500000 -o analyze.xtc

conda activate gmxmmpbsa

nohup mpirun --allow-run-as-root -np 32 gmx_MMPBSA -O -i PBmmpbsa.in -cs md.tpr -ci index.ndx -cg 1 13 -ct mmpbsa.xtc -cp topol.top &

###PB Pro-Pro(OPLSff) 8 Chain A 19 Chain B

mpirun --allow-run-as-root -np 18 gmx_MMPBSA -O -i PBPro-Pro.in -cs ../49700.pdb -ct ../md.xtc -ci ../prolig_center.ndx -cg 18 19 -cp ../topol.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv