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 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.