Coarse grained simulation of a water system

• started on Step 5 from MARTINI tutorial: http://cgmartini.nl/index.php/tutorials-general-introduction-* * * gmx5/proteins-gmx5
• gmx solvate -cp minimization -vac.gro -cs water.gro -radius 0.21 -o solvated.gro

all these files were uploaded from their files

• edited “topol.top”

changed SOL to 3881 because # of atoms were matched from solvated.gro

• compared system.top from “cd martiniamino” to “topol.top” from martiniwater
• edited “topol.top”

put “#include “martini_v2.2.itp”” and removed SOL and put W

• gmx grompp -p topol.top -c solvated.gro -f minimization.mdp -o minimization.tpr
• gmx mdrun -deffnm minimization -v

Information from previous command:

potential energy = -1.1218470e+05

maximum force = 1.1551949e+02

norm of force = 6.7654659e+00

• gmx grompp -p topol.top -c minimization.gro -f equilibration.mdp -o equilibration.tpr
• vmd equilibration.gro dynamic.xtc