Hello all, I carried out a molecular dynamics simulation for a coarse grained membrane system. I want to select the PO4 groups in top and bottom leaflets and calculate the vertical distance. How can I command it using gmx select and gmx distance?
Additionally, I converted md.gro file to .pdb file and separated the PO4 groups in top and bottom leaflets into two clusters on Matlab. Can I use the vertical distance between center of mass of two clusters as bilayer thickness, is it comparable to experimental results?
You can use gmx select with -oi option (or -oc option. But it may be easy to use -oi).
Regarding the bilayer thickness...The vertical distance between centre of mass of two clusters may match with experimental result...But it is hard to say without seeing the structure...
Gülşah Gül
Thank you Aadhityan Arivazhagan and Pritam Kumar Panda
but I handled it. Let me share it for those interested in the subject:I generated a selection.dat file which includes:
top_po4 = name PO4 and (z > 5); (Here 5 nm is middle of my pbc box)
bot_po4 = name PO4 and (z < 5);
top_po4;
bot_po4;
Then commanded:
gmx select -sf selection.dat -f md.xtc -s md.tpr -on po4_index.ndx
gmx distance -f md.xtc -s md.tpr -n po4_index.ndx -select 'com of group 0 plus com of group 1' -oxyz po4_distance.xvg
Alternatively, there is a perl script for bilayer separation here: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/scripts.html
[Just adding on here] And a python script: https://github.com/jbarnoud/splitleafs
Hi Gülşah Gül , could you clarify a bit more about the format of your 'selection.dat' file? What is exactly "name PO4", is it atom name or molecule name? (e.g. my bilayer contains 72 POPC molecules, I want to get index for P atom, so is the name P or POPC?) Could you please provide the first few lines of the selection.dat file as an example? Thank you very much for your help.
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