I used gromacs to perform a 10 ns equilibration of POPC membrane. I've heard that we can use gmx density to get the bilayer thickness. I would be very grateful if anyone can suggest me how to use it to measure bilayer thickness. Thanks
Prepare an index group with only the P atoms of your head groups. Feed that and the trajectory into gmx density. Compute the density along the bilayer normal (-d z) of the P atoms. Calculate the distance between the peaks in the density profile. This way you get the average P-P distance, which is used to describe bilayer thickness. (for example here: http://aip.scitation.org/doi/abs/10.1063/1.472323) You might want to increase the number of slabs and use the center and symm functions of gmx density.
Thanks Eric, Thanks a lot. I used gmx make_ndx -f NPT_bilayer_par.tpr -o density_groups.ndx and then chose aP for Phosphorous. Any suggestions to increase the number of slabs and using the center and symm functions of gmx density ?
The answer is to get used to the -h command and the GROMACS documentation.
gmx density -h clearly tells you:
"-sl (50) Divide the box in this number of slices."
So you can use -sl 100 to increase the number of slices to 100 for example while the default is 50.
You may want to try the 'GridMAT' program. Here is the link:
http://www.bevanlab.biochem.vt.edu/GridMAT-MD/
Thanks Swapnil, I did use Gridmat as well, but I am having a hard time installing matpack for analysis purposes.
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