normal Why I got water in the centre with DPPC on the two sides?

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1 year 6 months ago #7984 by lanselibai
I am following the exactly same as "Bilayer self-assembly" in the cgmartini.nl/index.php/tutorials-general...n-gmx5/bilayers-gmx5

However, after the 30 ns, I got water molecules in the centre with DPPC on the two ends.

Is this normal?

Here is my graph
github.com/lanselibai/martini/blob/master/1.png

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1 year 6 months ago #7990 by bart
You didn't take the PBC into account. All is fine if you shift the box with half z.

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1 year 6 months ago #7991 by riccardo

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1 year 6 months ago #7992 by lanselibai
Thank you very much! I got that!

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7 months 2 weeks ago #8388 by TravisM
Hi all,

I apologize for ressurecting an old thread, but I figured it was better than creating a new thread for the exact same topic.

My simulation resulted in the same situation (lipid-lipid interaction spans pbc) - however, I cannot for the life of me figure out how to adjust the trajectories to center everything. I have tried many combinations of

gmx trjconv -f .xtc -s .tpr -o .gro -trans 3.75 0 0
OR
gmx trjconv -f .xtc -s .tpr -o .gro -shift 3.75 0 0

With different x values for the shift/translate vector without observing any changes when visualizing the system in VMD. I was able to get a visualization of the bilayer using -pbc res as an option to trjconv. However, this placed a series of headgroups along the boundary and all of the water molecules on a single side. For aesthetic purposes I would love to get a trajectory where the water beads are located at the edges of the simulation box with the lipids in the center.

I am brand new to Linux/GROMACS/MARTINI so if nothing else I figured this is good experience learning to manipulate pbcs.

Thanks!
Travis

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7 months 5 days ago #8394 by riccardo
Hi, please have a look at this thread about the same issue www.cgmartini.nl/index.php/component/kun...ide-and-water-inside

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