[gmx-users] Re: Leaflet of Bilayer

Nicolas Sapay nsapay at ucalgary.ca
Fri Sep 19 19:48:29 CEST 2008


minnale wrote:
>
>  
>
>
> 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
>
It's probably because your system is not center on 0.0. By default, 
Gromacs center boxes on lenght/2
>
>
> 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.
> >
> >Nicolas
>
>
> >
> > >
> > >> 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
>
>
>
> Ebay 
> <http://adworks.rediff.com/cgi-bin/AdWorks/click.cgi/www.rediff.com/signature-home.htm/1050715198@Middle5/2401775_2394076/2397136/1?PARTNER=3&OAS_QUERY=null> 
>
>
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