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