[gmx-users] Radial Distribution Function of DPPC Bilayer

[Nidhin Thomas]

Dear Gromacs Users,

I have simulated a DPPC bilayer using charmm-gui.org. I ran the simulation
for about 180 nano seconds. I had used the mdp files which were provided by
charmm-gui (used vdw force-switch cut-off range as 10-12 A).

I have to find out the radial distribution of Phosphorus-Phosphorus (P-P)
pairs. Therefore, I created the index files for phosphorus atoms of DPPC
lipids in each leaflet and used following command to obtain radial
distribution function.

gmx_mpi rdf -f DPPC.xtc -s DPPC.tpr -n PN-index.ndx -o P-P_rdf.xvg -b
120000 -e 180000 -bin 0.05

I chose all phosphorus atoms of one leaflet as both ‘ref’ and ‘sel’.

Is this the correct command to obtain the radial distribution function of
P-P pairs?

I obtained a radial distribution plot, which I have uploaded in the
following link. I compared the same with the paper: doi:
10.1016/S0006-3495(03)75094-2
<http://dx.doi.org/10.1016%2FS0006-3495(03)75094-2>. But the force field
and other parameters were different for this paper. I was hoping for a
similar plot but the peak value of my plot seem very different. I also
simulated a DPPC bilayer using GROMOS96 53a6 force filed for 180 ns. The
three dimensional radial distribution for this system is also provided in
the figure.

I have also uploaded the part of log files. Could anyone please let me know
what am I doing wrong in selecting the parameters?

https://www.dropbox.com/sh/hz0ryxeyptf74la/AAD-OKUwauoWO84mlE5_lycha?dl=0

Thank you for the help!

Nidhin Thomas

University of Houston