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 z0] 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 z0] 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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