[gmx-users] gromacs.org_gmx-users Digest, Vol 147, Issue 178

[Nidhin Thomas]

>
> Hi Dr. Justin,
>

Thanks a lot for the quick reply.

I have also used -xy  option to get the two dimensional distribution. The
peak value of the distribution change considerably in this case. I have
uploaded the images below. For GROMOS force field, the shape of the
distribution also changes. I thought I was doing something wrong in
selecting the parameters.

https://www.dropbox.com/s/gy85g7wyvavp24v/RDF-2D.png?dl=0

Thanks again!

Nidhin Thomas



> Message: 6
> Date: Fri, 29 Jul 2016 20:04:24 -0400
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Radial Distribution Function of DPPC Bilayer
> Message-ID: <7f94e201-0fe7-e6bf-4e1b-40a7bf03c5ee at vt.edu>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
>
>
> 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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> End of gromacs.org_gmx-users Digest, Vol 147, Issue 178
> *******************************************************
>