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I have a basic question regarding CG water in Martini. I typically use CHARMM-GUI to implement Martini for my proteins, but now I’m exploring the Go-Like model. I followed the tutorial, but I’m stuck at the solvation step: gmx solvate -cp minimization-vac.gro -cs water.gro -radius 0.21 -o solvated.gro
The tutorial mentions using pre-existing .gro files for solvation. Is this process independent of the box size? For example, I am working with a multimeric system. Additionally, the tutorial refers to pre-prepared NaCl+water boxes with specific charge configurations. How can I customize these parameters for my system?
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Martini Force Field Initiative
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I have a basic question regarding CG water in Martini. I typically use CHARMM-GUI to implement Martini for my proteins, but now I’m exploring the Go-Like model. I followed the tutorial, but I’m stuck at the solvation step:
gmx solvate -cp minimization-vac.gro -cs water.gro -radius 0.21 -o solvated.groThe tutorial mentions using pre-existing .gro files for solvation. Is this process independent of the box size? For example, I am working with a multimeric system. Additionally, the tutorial refers to pre-prepared NaCl+water boxes with specific charge configurations. How can I customize these parameters for my system?
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