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bilayer thickness
- gourav
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12 years 8 months ago #766
by gourav
bilayer thickness was created by gourav
hi,
i tried to find the thickness of bilayer which is provided in the tutorial (dspc_bilayer.gro), these are my commands:
>>>make_ndx -f dspc_bilayer.gro -o index.ndx
i made PO4 as one of the group in this step(it was 128 elements)
>>>g_density -n index.ndx -o martini.xvg
i selected PO4
and the plot which i got was exactly similar to the plot which i got from the bilayer set up by me,both were having many peaks.......still confused about calculating thickness on basis of this plot, kindly help
Thanking you in advance
i tried to find the thickness of bilayer which is provided in the tutorial (dspc_bilayer.gro), these are my commands:
>>>make_ndx -f dspc_bilayer.gro -o index.ndx
i made PO4 as one of the group in this step(it was 128 elements)
>>>g_density -n index.ndx -o martini.xvg
i selected PO4
and the plot which i got was exactly similar to the plot which i got from the bilayer set up by me,both were having many peaks.......still confused about calculating thickness on basis of this plot, kindly help
Thanking you in advance
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- djurre
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12 years 8 months ago #767
by djurre
Replied by djurre on topic bilayer thickness
Dear gourav,
It is not completely clear to me what exactly you did.
Did you do the analysis on 'dspc_bilayer.gro' or on 'traj.xtc'. Note that the command as you posted it will automatically look for 'traj.xtc'.
If you actually did the analysis on the .gro file, that might explain the many peaks: they are just noise due to the lack of sampling in one frame.
If you did the analysis on the .xtc I don't understand what is wrong. What is along the x-axis? (Hopefully nm's from 0 to ~7nm) At which positions are the peaks?
It is not completely clear to me what exactly you did.
Did you do the analysis on 'dspc_bilayer.gro' or on 'traj.xtc'. Note that the command as you posted it will automatically look for 'traj.xtc'.
If you actually did the analysis on the .gro file, that might explain the many peaks: they are just noise due to the lack of sampling in one frame.
If you did the analysis on the .xtc I don't understand what is wrong. What is along the x-axis? (Hopefully nm's from 0 to ~7nm) At which positions are the peaks?
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- jantunes
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12 years 4 months ago #847
by jantunes
Replied by jantunes on topic bilayer thickness
I had the same problem in the first time i tried, because the membrane normal was in the X axis, so i needed to add the -d X flag ;).
Ex: g_density -f traj.xtc -s topol.tpr -n index.ndx -o density.xvg -d X
Ex: g_density -f traj.xtc -s topol.tpr -n index.ndx -o density.xvg -d X
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