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. > >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
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