Size of the box is increasing

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I am working on coarse grain martini protein simulation. I want to set box shape as orthorhombic but this command is not working : gmx editconf -f Protein_A-CG.pdb -o Protein_A-CG.gro -c -bt orthorhombic. Apart from that, the box dimension is changing throughout the simulation: Initial Box dimension: 76.196 76.196 76.196. * Energy Minimization (em.gro): 11.04000 10.86030 11.10520

  • NVT Equilibration (nvt.gro): 11.04000 10.86030 11.10520

  • NPT Equilibration (npt.gro): 10.14378 9.97867 10.20369

  • MD Production Run (md.gro): 10.34668 10.17827 10.40779
    Infact initially only the output file of Protein_A-CG.gro the box dimension changes. Can you suggest me how should i fix both the problems 1) orthrhombic 2) Changing of box size throughout the simulation.

2

Without more information it’s very difficult to say why the command is not working. Do you get any error output? Since you are creating a new box you would probably have to define its new size. Since you want an orthorhombic box you probably want to base the box size on the size of the protein. Try, e.g.:
gmx editconf -f Protein_A-CG.pdb -o Protein_A-CG.gro -d 1.2 -bt orthorhombic

Why are you worried about the box size changing? If you don’t want that, then continue the simulations in the NVT ensemble. Simulations run in the NPT ensemble (assuming also that your production run is in the NPT ensemble) keep the pressure by changing the box size.