Gromacs
Note: The steps in this document were written for Gromacs 4.
Steps to carry out an explicit solvent simulation
# Convert the structure from PDB to Gromacs format
pdb2gmx -ignh -f cts1.pdb
# Build the simulation box
editconf -bt octahedron -f conf.gro -o box.gro -c -d 1.0
genbox -cp box.gro -cs spc216.gro -o solvated.gro -p topol.top
# Fill the box with counter ions to neutralize the overall charge
grompp -f ions.mdp -c solvated.gro -p topol.top -o ions.tpr
genion -s ions.tpr -o ions.gro -p topol.top -pname NA -np 1 -nname CL -nn 8 -g ion.log -neutral
# Carry out energy minimization
grompp -f em.mdp -c ions.gro -p topol.top -o em.tpr
mdrun -v -deffnm em
# Constant temperature equilibration
grompp -f nvt.mdp -c em.gro -p topol.top -o nvt.tpr
mdrun -v -deffnm nvt
# Constant pressure equilibration
grompp -f npt.mdp -c nvt.gro -t nvt.cpt -p topol.top -o npt.tpr
mdrun -v -deffnm npt
# Production MD run
grompp -f md.mdp -c npt.gro -t npt.cpt -p topol.top -o md.tpr
mdrun -v -deffnm md
Restart Crash Run
Energy calculation
g_energy -f run.edr -o energy.xvg -b 0 -e 1000 -skip 5
g_energy -f md_0.edr -o md_0-energy.xvg -skip 5
# for 50 ns
g_energy -f md_2.edr -o md_2-energy.xvg -b 0 -e 50000 -skip 5
Radius of Gyration
g_gyrate -f run.xtc -s run.tpr -o gyrate.xvg -b 0 -e 1000
g_gyrate -f md_0-fit.xtc -s em.tpr -o md_0-gyrate.xvg -ncskip 5
RMSD Calculation
RMSF Calculation
g_rmsf -f run.xtc -s run.tpr -b 0 -e 10000 -o rmsf.xvg
# for residue
g_rmsf -s em.tpr -f run.xtc -o rmsf.xvg -b 0 -e 1000 -res
Parallel Run
Extending finished run
tpbconv -s previous.tpr -extend timetoextendby -o next.tpr
mdrun -s next.tpr -cpi previous.cpt
# for 50ns
tpbconv -s md_2-ext.tpr -extend 50000 -o md_2-ext-150.tpr
Trajectory concatanate
Box centering
trjconv -s em.tpr -f nvt.trr -o md_nojump.xtc -pbc nojump -boxcenter tric
trjconv -s md.tpr -f md.trr -o md_nojump.xtc -pbc nojump -center
g_trjconv -s run_3.tpr -f run_3.trr -o run_3.xtc -pbc mol -ur compact -center
Fit the tragectory to the initial structure to avoid PBC effects
trjconv -s run.tpr -f run.xtc -o run-fit.xtc -fit progressive
# For Complex (first fit one complex then the other)
trjconv -s md.tpr -f md.trr -o md_nojump.xtc -pbc nojump -center
trjconv -s em.tpr -f md_0-protein.xtc -o md_0-acp-fit.xtc -fit progressive -n acpIndex.ndx
Making index file
make_ndx -f conf.gro -o index.ndx
# Choose the group and then define the residues using && with the group number
Measure distance between atoms overtime
Essential Dynamics Analysis
g_covar -s run.tpr -f run.xtc
# Choose option for backbone or for protein
# the output will be in eigenval.xvg and eigenvec.trr
xmgrace eigenval.xvg
# to visualize the number of modes contributing to the overall fluctuation
g_anaeig -extr extr_ev1.pdb -first 1 -last 1 -nframes 10 -s run.tpr -f run.xtc
pymol extr_ev1.pdb
# If we are interested in the time evolution of these collective coordinates during the simulation, we can project the trajectory onto these coordinates:
g_anaeig -proj -s run.tpr -f run.xtc
xmgrace proj.xvg
trj_cavity v1
./trj_cavity -s em.tpr -f md_0-cat-fit.xtc -seed 45.750 50.943 30.368 -o md_0_cavity_max_dim5_ff1.3.pdb -ot md_0_cavity_max_dim5_ff1.3.xtc -ov md_0_volume_max_dim5_ff1.3.xvg -mode max -dim 5 -ff_path amber99sb-ildn.ff -ff_radius -spacing 1.3 -cutoff 9 -n index.ndx