<P>
<BR>
Thanks for the response<BR>
Just diverting this topic to about specific number of popc molecules.<BR>
<BR>
I created the bilayer by using genconf command <BR>
genconf -f popc128a.pdb -o out.gro -dist 0 0 0 -nbox 2 1 1 (as I posted in my previous mail) generated output file contain 128 popc in each leaflet of bilayer. <BR>
<BR>
If you see original popc box dimensions 6.1x6.2x6.9 (means in all dimensions popc number almost same)but with genconf command above mentioned options created box values 12x6.1x6.9. I dont want that many popc molecules because in X-dimension too many popc molecules are present. <BR>
<BR>
1.is there anyway to reduce those popc molecules from 128 to 80/90 popc molecules? or <BR>
2.I wanted to create popc molecules 80 or 90 in eachleaflet is it possible to generate?<BR>
<BR>
These are may be trivial queries<BR>
Could you give suggest me please<BR>
Thanks in advance.<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>
>>It's probably because your system is not center on 0.0. By default, Gromacs center boxes on lenght/2<BR>
>It's probably because your system is not centered on 0.0. By default, Gromacs centers boxes on lenght/2<BR>
>.. Sorry for the grammar, I'm not well awake this morning.<BR>
>>><BR>
>>><BR>
>>>Thanks in advance.<BR>
>>>e<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>
>>><BR>
>>><BR>
>>><BR>
>>>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> <BR>
>>><BR>
>>>------------------------------------------------------------------------<BR>
>>><BR>
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