normal recentering the protein

  • cm
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1 year 1 month ago #7599 by cm
recentering the protein was created by cm
hi,
i have two protein in a waterbox and i am following martini protein tutorial.
genbox -cp minimization-vaccum.gro -cs water-box-CG_303K-1bar.gro -vdwd 0.21 -o system-solvated.gro
afte this command when i saw the system-solvated.gro file in vmd.it was shown that one of the protein is out of the water box.how i can place the proteins in the center of the water box.

thanking you

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1 year 1 month ago #7600 by peterkroon
Replied by peterkroon on topic recentering the protein
Hi cm,

there is no such thing as outside the box due to periodic boundary conditions. See www.gromacs.org/Documentation/Terminolog..._Boundary_Conditions

You can put your protein in the center of your box using editconf for single frames and trjconv for trajectories. But just to reiterate, it won't matter for your simulation.

Peter

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1 year 1 month ago #7602 by cm
Replied by cm on topic recentering the protein
thank you so much for your information.

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