normal peptide at the corner of box

  • roshanak
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2 years 6 months ago #6034 by roshanak
peptide at the corner of box was created by roshanak
hi. i'm beginner in martini simulation.
i do tutorial's protein that is in this address: www.cgmartini.nl/index.php/tutorials-gen...ion/proteins#martini
and reach to production run step (7 step).when i look at the "dynamic.gro" file, with vmd, i see peptide at the corner of box.what is its reason? do i have to do equilibration step on "dynamic.gro" file?
thank you.

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2 years 5 months ago #6555 by peterkroon
Replied by peterkroon on topic peptide at the corner of box
Hi,

dynamic.gro is the last frame produced by `mdrun -deffnm dynamic -v`. So no, it makes no sense to run equilibration on that. You'll find the associated trajectory in `dynamic.xtc` (or .trr).

Due to periodic boundary conditions, there are no corners in your simulation box. VMD might show them, but they're not really there.

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