Re: Re: [gmx-users] Re: Leaflet of Bilayer

2008-09-21 Thread minnale 
  
Thanks for the response
Just diverting this topic to about specific number of popc molecules.

I created the bilayer by using genconf command 
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. 

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.   

1.is there anyway to reduce those popc molecules from 128 to 80/90 popc 
molecules? or 
2.I wanted to create popc molecules 80 or 90 in eachleaflet is it possible to 
generate?

These are may be trivial queries
Could you give suggest me please
Thanks in advance.


>>>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 
>>>>> PROTECTED]/2401775_2394076/2397136/1?PARTNER=3&OAS_QUERY=null> 
>>>
>>>
>>>
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>>
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Re: [gmx-users] Re: Leaflet of Bilayer

2008-09-19 Thread 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 
 





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Re: [gmx-users] Re: Leaflet of Bilayer

2008-09-19 Thread Nicolas Sapay 

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



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



Ebay 
 





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begin:vcard
fn:Nicolas SAPAY
n:SAPAY;Nicolas
org:University of Calgary;Biological Sciences
adr:;;2500 University drive NW;Calgary;AB;T2N 1N4;Canada
email;internet:[EMAIL PROTECTED]
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tel;work:(403) 220-6869
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