/home/zwei/work/MD/MORC16/MARTINI/

vmd

source martini_morc16.tcl

output:martini_morc16.gro

We will build a box with size of 20nm*20nm*20nm.

gmx_mpi insert-molecules -ci martini_morc16.gro -box 20 20 20 -nmol 1280 -o 1280_noW.gro

gmx_mpi grompp -f minimization.mdp -c 1280_noW.gro -p MOC.top -o moc-min-init.tpr

gmx_mpi mdrun -deffnm moc-min-init -v -c 1280_minimized.gro

gmx_mpi solvate -cp 1280_minimized.gro -cs water.gro -o waterbox.gro -maxsol 7680 -radius 0.21

gmx_mpi grompp -f minimization.mdp -c waterbox.gro -p MOC.top -o moc-min-solvent.tpr

gmx_mpi mdrun -deffnm moc-min-solvent -v -c minimized.gro

gmx_mpi grompp -f martini_md.mdp -c minimized.gro -p MOC.top -o moc-md.tpr

gmx_mpi mdrun -deffnm moc-md -v

gmx_mpi trjconv -f moc-md.xtc -s moc-md.tpr -skip 10 -o skip10.xtc

gmx_mpi trjconv -s moc-md.tpr -f skip10.xtc -center -pbc whole -dump 0 -o moc-md-start.gro

gmx_mpi trjconv -s moc-md.tpr -f skip10.xtc -o moc-md-center.xtc -pbc mol -trans 100 100 255

vmd moc-md-start.gro moc-md-center.xtc

 

now let's try a system with more lipids and bigger box. 

gmx_mpi insert-molecules -ci martini_morc16.gro -box 50 50 50 -nmol 12800 -o 12800_noW.gro

gmx_mpi grompp -f minimization.mdp -c 12800_noW.gro -p MOC.top -o moc-min-init.tpr

gmx_mpi mdrun -deffnm moc-min-init -v -c 12800_minimized.gro

gmx_mpi solvate -cp 12800_minimized.gro -cs water.gro -o 12800waterbox.gro -maxsol 768000 -radius 0.21

gmx_mpi mdrun -deffnm moc-min-solvent -v -c minimized.gro

gmx_mpi grompp -f martini_md.mdp -c minimized.gro -p MOC.top -o moc-md.tpr

gmx_mpi mdrun -deffnm moc-md -v

 

 

gmx_mpi insert-molecules -ci martini_morc16.gro -box 100 100 100 -nmol 12800 -o 12800_noW.gro

gmx_mpi grompp -f minimization.mdp -c 12800_noW.gro -p MOC.top -o moc-min-init.tpr

gmx_mpi mdrun -deffnm moc-min-init -v -c 12800_minimized.gro

gmx_mpi solvate -cp 12800_minimized.gro -cs water.gro -o 12800waterbox.gro -maxsol 4768000 -radius 0.21

gmx_mpi mdrun -deffnm moc-min-solvent -v -c minimized.gro

 

 

Add one Na ion to water box

gmx_mpi insert-molecules -ci martini_morc16.gro -box 20 20 20 -nmol 1280 -o 1280_noW.gro

gmx_mpi grompp -f minimization.mdp -c 1280_noW.gro -p MOC.top -o moc-min-init.tpr

gmx_mpi mdrun -deffnm moc-min-init -v -c 1280_minimized.gro

gmx_mpi solvate -cp 1280_minimized.gro -cs water.gro -o waterbox.gro -maxsol 100000 -radius 0.21

(50218 W)

replace last two CG water to NA+ and CL-

51497ION    NA+66857  19.123  19.476  18.778
51498ION    CL-66858  18.966  19.730  18.325

gmx_mpi grompp -f minimization.mdp -c waterbox.gro -p MOC.top -o moc-solvent-ion.tpr

gmx_mpi mdrun -deffnm moc-solvent-ion -v -c minimized.gro

gmx_mpi grompp -f martini_md.mdp -c minimized.gro -p MOC.top -o moc-md.tpr

gmx_mpi mdrun -deffnm moc-md -v

 

simulation with ions fixed in the center of box.

NA+	CL-

 

 

2) change the cg_bonds.tcl script. Change line 491 from
set gmxdump "/path/to/gromacs4/bin/gmxdump"
to
set gmxdump "/path/to/gromacs5/bin/gmx_mpi dump"