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recentering the protein
- cm
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5 years 11 months 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
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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- peterkroon
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5 years 11 months 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
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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- cm
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5 years 11 months ago #7602
by cm
Replied by cm on topic recentering the protein
thank you so much for your information.
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