[gmx-users] Leaflet of Bilayer

[Nicolas Sapay]

Justin A. Lemkul wrote:
>
>
> minnale wrote:
>>  
>>
>> 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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>>  >
>>  >--
>>  >************************************************
>>  >Dr. Jochen Hub
>>  >Max Planck Institute for Biophysical Chemistry
>>  >Computational biomolecular dynamics group
>>  >Am Fassberg 11
>>  >D-37077 Goettingen, Germany
>>  >Email: jhub[at]gwdg.de
>>  >Tel.: +49 (0)551 201-2312
>>  >************************************************
>>
>>
>>
>>
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