[gmx-users] Re: Leaflet of Bilayer
minnale_gnos at rediffmail.com
Fri Sep 19 19:34:20 CEST 2008
Thanks Justin and Nicolas for gave suggestions.
I have tried with Nicolas suggested command in VMD Tkconsole, its showing whole popc molecules but not leaflet. I typed the command in Tkconsole like this
[atomselect top "name P8 and z>0"] num
it has showed 201, means the total number popc molecues in the .gro file.
Could you tell any suggestion
Thanks in advance.
> >> Hi Jochen thanks for your reply
> >> I have gone through this recent mail
> >> http://www.gromacs.org/pipermail/gmx-users/2008-September/036508.html
> >> more over if I use genconf command like this
> >> genconf -f .gro -o out -nbox 2 1 1 -dist 0 0 0 its adding 128 in
> >> eachleaflet I dont wany that many popc molecules.
> >> 1.Is it wrong if I increase the popc molecules by using genbox?
> > It is best to use genconf, because then the periodic images of the
> > unit cell remain intact, that is, since you're using a
> > pre-equilibrated bilayer, it's better to not snip chunks out of it.
> > You can deal with that by sufficient equilibration, however.
> > It is also easier to use genconf, because you then know exactly how
> > many lipids you are dealing with (in regards to your previous
> > message). You could probably write some script to tell you which
> > lipid is in a given leaflet based on whether a certain atom (i.e., P8
> > or something else) is above or below the center of the bilayer.
>In case you use VMD, you can get the number of phospholipid per leaflet
>with the following command:
> [atomselect top "name P8 and z>0"] num
>This will give you the number of PC in the upper leaflet, assuming 1)
>the phosphorus atom is named P8 and 2) the bilayer is center on 0.0
>along the z axis.
> >> 2.Is there anyway to increase popc and water numbers by mentioning
> >> specific molecules number?
> > Not that I'm aware of. There is a -maxsol option in genbox, but that
> > is for capping the amount of water molecules added to a box.
> > -Justin
> >> Could you suggest me
> >> Thanks in advance.
> >> On Fri, 19 Sep 2008 Jochen Hub wrote :
> >> >minnale wrote:
> >> > >
> >> > > Hi all,
> >> > > I have extended popc bilayer(intial popc.pdb from Dr.Tielmen
> >> site) by using genbox command, I issued
> >> > > genbox -cs popc128a.gro -o out.gro -box 9.2 9.2 6.9 it ran
> >> successfully with increase of popc and water molecules.
> >> > > Now I want to visualise this out file in VMD in a way that in
> >> eachleaflet how many popc molecules and water residues are there, May
> >> be this is trivial query.
> >> > > Could you give me suggestion.
> >> >
> >> >If you want to enlarge a membrane patch, use genconf. Not genbox!
> >> >
> >> >jochen
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