hello.
I used charmm-gui for building micelle-protein complex.
I increased carbon radius for removing water inside the micelle. but nothing happend! Should I do something with charmm-gui to build a correct structure without water inside it?
the following picture showes water density in the box, water density should be zero at the center of the micelle!!
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You are best directing this question to those who provide the charmm-gui, this is not a GROMACS issue.
I know it isn’t gromacs issue. But I thought maybe some body had the same problem who can help me now.
Anyway, Thank you.
Hi - depending on what you’re trying to study, if you just run the simulation for a while the water will eject eventually. You could restrain the micelle atoms in the meantime.
Thanks for your response. I ran the simulation for more 100 ps but water density increased at the center of the structure even though my structure seems more compact than before!!
my first structure:
after simulation:
You wouldn’t expect to see ejection on that timescale, more like 10s to 100s of nanoseconds. Also what is your coordinate/command for gmx density?
Thank you so much…
So you think nothing is wrong with the initial structure and it’s just about timescale.
This is my command:
gmx density -s nvt.tpr -f nvt.xtc -o dens_nvt.xvg -d Z
If you’re slicing along the z dimension, but your micelle doesn’t cover the entire box in that dimension (which it wouldn’t because it has finite size), gmx density is also picking up the waters in those z-slabs outside of the micelle. I think you’re just misinterpreting gmx density
Thank you kevin. All bests for you:)