[gmx-users] Radial Distribution Function of DPPC Bilayer

[Justin Lemkul]

On 7/29/16 6:44 PM, Nidhin Thomas wrote:
> 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
>

You're using a different force field and you're getting a different result. 
There's nothing wrong here.

You may want to use -xy in your calculations to get the in-plane RDF, but that 
won't have a large effect on the outcome.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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