I am running a protein ligand MD simulation using two ligands in gromacs, but when I prepared solv.gro and newbox.gro my protein is not central inside the water box.
I used following commands:
gmx_mpi editconf -f complex.gro -o newbox.gro -bt dodecahedron -d 1.0
gmx_mpi solvate -cp newbox.gro -cs spc216.gro -p topol.top -o solv.gro
Please suggest
You could use -center along with the gmx editconf or gmx trjconv -center -pbc whole. However, you might want to go through the manual before you actually use gmx trjconf as the program will ask for a ".tpr" file.
I hope you are aware of the gromacs documentation for each of the commands describing all the possible tags that can be used. For editconf, you find it here: http://manual.gromacs.org/programs/gmx-editconf.html
Using -center centers the protein in the box you define.
You should add -c in your commands. and to check it you can use -center x y z.... more info:http://www.gromacs.org/@api/deki/files/206/=membrane_tutorial_online.pdf
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