[gmx-users] Re: Leaflet of Bilayer

[Nicolas Sapay]

Nicolas Sapay wrote:
> 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
It's probably because your system is not centered on 0.0. By default, 
Gromacs centers boxes on lenght/2
.. Sorry for the grammar, I'm not well awake this morning.
>>
>>
>> Thanks in advance.
>> e
>> > >>
>> > >> 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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