This program is a tool to generate alginate or chitosan coarse-grained topology files for GROMACS. The model describes the polyelectrolytes alginate and chitosan and their polyelectrolyte complexes in an implicit solvent.
More information can be found at https://ntnuopen.ntnu.no/ntnu-xmlui/handle/11250/3016417
MDAnalysis
Generate topolgy files for a length 10 alginate
python topogen.py 'MGMGMGMMMG' 10-alginate
# IMPORTANT! Replace stiff bonds by restraints
# Make bonds2constr executable! (e.g. chmod +x bonds2constr.sh)
./bonds2constr.sh outfiles/10-alginate.itp outfiles/10-alginate.itp
Setting up and running a system in GROMACS containing
- 2 alginate chains of length 10
- 2 chitosan chains of length 3
- ions to neutralize each oligomer individually
python topogen.py 'MMMMMMMMMM' 10-alginate
python topogen.py 'YYY' 3-chitosan
# IMPORTANT! Replace stiff bonds by restraints
./bonds2constr.sh outfiles/10-alginate.itp outfile/10-alginate.itp
./bonds2constr.sh outfiles/3-chitosan.itp outfiles/3-chitosan.itp
cd example
gmx editconf -f ../outfiles/10-alginate.gro -box 8 -bt cubic -o tmp.gro
gmx insert-molecules -f tmp.gro -ci ../outfiles/10-alginate.gro -nmol 1 -o tmp.gro
gmx insert-molecules -f tmp.gro -ci ../outfiles/3-chitosan.gro -nmol 2 -o tmp.gro
gmx insert-molecules -f tmp.gro -ci ../forcefield/NA.gro -nmol 20 -o tmp.gro
gmx insert-molecules -f tmp.gro -ci ../forcefield/CL.gro -nmol 6 -o init-conf.gro
rm \#tmp.gro*
mkdir min
cd min
gmx grompp -f ../../mdps/min.mdp -c ../init-conf.gro -p ../top/topol.top -o min.tpr
gmx mdrun -deffnm min -v
cd ../
mkdir nvt
cd nvt
gmx grompp -f ../../mdps/nvt.mdp -c ../min/min.gro -p ../top/topol.top -o nvt.tpr
gmx mdrun -deffnm nvt -v