GROMACS version: 2019
GROMACS modification: Yes/No
Here post your question
Hi guys,
I have a simulation of protein-ligand system in dodecahedron box created by command gmx editconf -bt dodecahedron -c -d 1.2 -f rec.pdb -o rec.pdb. I want to expand box size to 300nm^3 for all system so how can I do that? It would be great if you can give me some refferences or guidelines to resolve this problem.
Thank you so much.
Nhina
During processing, editconf gives you the box dimensions and volume. If you want to have exactly 300 nm³ with the same box geometry, take your ratio of the desired and current volume, calculate the cubic square, and use the -scale sc_x sc_y sc_z option, placing the cubic square as the respective scaling factors. Then editconf should give you the desired box volume.
In case you already have solvent/ions/… in your system, discarding them and resolving from scratch might be easier, depending on where you are in the workflow.
thank you so much