Discussion:
Leaflet of Bilayer
(too old to reply)
minnale
2008-09-19 07:25:46 UTC
Permalink
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.
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Jochen Hub
2008-09-19 07:51:07 UTC
Permalink
Post by minnale
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
Post by minnale
------------------------------------------------------------------------
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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
************************************************
minnale
2008-09-19 09:09:20 UTC
Permalink
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?
2.Is there anyway to increase popc and water numbers by mentioning specific molecules number?
Could you suggest me
Thanks in advance.
Post by Jochen Hub
Post by minnale
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
Post by minnale
------------------------------------------------------------------------
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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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Justin A. Lemkul
2008-09-19 11:00:50 UTC
Permalink
Post by minnale
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.
Post by minnale
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
Post by minnale
Could you suggest me
Thanks in advance.
Post by Jochen Hub
Post by minnale
Hi all,
I have extended popc bilayer(intial popc.pdb from Dr.Tielmen
site) by using genbox command, I issued
Post by Jochen Hub
Post by minnale
genbox -cs popc128a.gro -o out.gro -box 9.2 9.2 6.9 it ran
successfully with increase of popc and water molecules.
Post by Jochen Hub
Post by minnale
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.
Post by Jochen Hub
Post by minnale
Could you give me suggestion.
If you want to enlarge a membrane patch, use genconf. Not genbox!
jochen
------------------------------------------------------------------------
Post by Jochen Hub
Post by minnale
_______________________________________________
gmx-users mailing list gmx-users at gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before
posting!
Post by Jochen Hub
Post by minnale
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-request at gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
************************************************
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
************************************************
------------------------------------------------------------------------
_______________________________________________
gmx-users mailing list gmx-users at gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
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--
========================================

Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================
Nicolas Sapay
2008-09-19 15:23:56 UTC
Permalink
Post by Justin A. Lemkul
Post by minnale
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
Post by Justin A. Lemkul
Post by minnale
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
Post by minnale
Could you suggest me
Thanks in advance.
Post by Jochen Hub
Post by minnale
Hi all,
I have extended popc bilayer(intial popc.pdb from Dr.Tielmen
site) by using genbox command, I issued
Post by Jochen Hub
Post by minnale
genbox -cs popc128a.gro -o out.gro -box 9.2 9.2 6.9 it ran
successfully with increase of popc and water molecules.
Post by Jochen Hub
Post by minnale
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.
Post by Jochen Hub
Post by minnale
Could you give me suggestion.
If you want to enlarge a membrane patch, use genconf. Not genbox!
jochen
------------------------------------------------------------------------
Post by Jochen Hub
Post by minnale
_______________________________________________
gmx-users mailing list gmx-users at gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search
before posting!
Post by Jochen Hub
Post by minnale
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-request at gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
************************************************
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
************************************************
------------------------------------------------------------------------
_______________________________________________
gmx-users mailing list gmx-users at gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the www
interface or send it to gmx-users-request at gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
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minnale
2008-09-19 17:34:20 UTC
Permalink
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

Thanks in advance.
Post by Nicolas Sapay
Post by Justin A. Lemkul
Post by minnale
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
[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
Post by Justin A. Lemkul
Post by minnale
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
Post by minnale
Could you suggest me
Thanks in advance.
Post by Jochen Hub
Post by minnale
Hi all,
I have extended popc bilayer(intial popc.pdb from Dr.Tielmen
site) by using genbox command, I issued
Post by Jochen Hub
Post by minnale
genbox -cs popc128a.gro -o out.gro -box 9.2 9.2 6.9 it ran
successfully with increase of popc and water molecules.
Post by Jochen Hub
Post by minnale
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.
Post by Jochen Hub
Post by minnale
Could you give me suggestion.
If you want to enlarge a membrane patch, use genconf. Not genbox!
jochen
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Nicolas Sapay
2008-09-19 17:48:29 UTC
Permalink
Post by minnale
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
Post by minnale
Thanks in advance.
Post by Nicolas Sapay
Post by Justin A. Lemkul
Post by minnale
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
[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
Post by Justin A. Lemkul
Post by minnale
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
Post by minnale
Could you suggest me
Thanks in advance.
Post by Jochen Hub
Post by minnale
Hi all,
I have extended popc bilayer(intial popc.pdb from Dr.Tielmen
site) by using genbox command, I issued
Post by Jochen Hub
Post by minnale
genbox -cs popc128a.gro -o out.gro -box 9.2 9.2 6.9 it ran
successfully with increase of popc and water molecules.
Post by Jochen Hub
Post by minnale
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.
Post by Jochen Hub
Post by minnale
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 at Middle5/2401775_2394076/2397136/1?PARTNER=3&OAS_QUERY=null>
------------------------------------------------------------------------
_______________________________________________
gmx-users mailing list gmx-users at gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
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Can't post? Read http://www.gromacs.org/mailing_lists/users.php
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Nicolas Sapay
2008-09-19 17:53:22 UTC
Permalink
Post by Nicolas Sapay
Post by minnale
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.
Post by Nicolas Sapay
Post by minnale
Thanks in advance.
e
Post by Nicolas Sapay
Post by Justin A. Lemkul
Post by minnale
Hi Jochen thanks for your reply
I have gone through this recent mail
http://www.gromacs.org/pipermail/gmx-users/2008-September/036508.html
Post by Nicolas Sapay
Post by Justin A. Lemkul
Post by minnale
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
Post by Nicolas Sapay
Post by Justin A. Lemkul
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
[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
Post by Justin A. Lemkul
Post by minnale
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
Post by Nicolas Sapay
Post by Justin A. Lemkul
is for capping the amount of water molecules added to a box.
-Justin
Post by minnale
Could you suggest me
Thanks in advance.
Post by Jochen Hub
Post by minnale
Hi all,
I have extended popc bilayer(intial popc.pdb from
Dr.Tielmen
Post by Nicolas Sapay
Post by Justin A. Lemkul
Post by minnale
site) by using genbox command, I issued
Post by Jochen Hub
Post by minnale
genbox -cs popc128a.gro -o out.gro -box 9.2 9.2 6.9 it ran
successfully with increase of popc and water molecules.
Post by Jochen Hub
Post by minnale
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
Post by Nicolas Sapay
Post by Justin A. Lemkul
Post by minnale
be this is trivial query.
Post by Jochen Hub
Post by minnale
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 at Middle5/2401775_2394076/2397136/1?PARTNER=3&OAS_QUERY=null>
------------------------------------------------------------------------
_______________________________________________
gmx-users mailing list gmx-users at gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the www
interface or send it to gmx-users-request at gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
_______________________________________________
gmx-users mailing list gmx-users at gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
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Can't post? Read http://www.gromacs.org/mailing_lists/users.php
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minnale
2008-09-21 16:52:38 UTC
Permalink
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.
Post by minnale
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.
Post by minnale
Thanks in advance.
e
Post by Nicolas Sapay
Post by Justin A. Lemkul
Post by minnale
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
[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
Post by Justin A. Lemkul
Post by minnale
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
Post by minnale
Could you suggest me
Thanks in advance.
Post by Jochen Hub
Post by minnale
Hi all,
I have extended popc bilayer(intial popc.pdb from Dr.Tielmen
site) by using genbox command, I issued
Post by Jochen Hub
Post by minnale
genbox -cs popc128a.gro -o out.gro -box 9.2 9.2 6.9 it ran
successfully with increase of popc and water molecules.
Post by Jochen Hub
Post by minnale
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.
Post by Jochen Hub
Post by minnale
Could you give me suggestion.
If you want to enlarge a membrane patch, use genconf. Not genbox!
jochen
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chris.neale
2008-09-22 05:55:37 UTC
Permalink
In my opinion, use any technique that you want (genbox included) then
run the resulting system for >=50ns while plotting the area per lipid
and order parameters over time. When these values stop drifting over
time then you have an equilibrated bilayer. If you have access to a
cluster that scales well to 4 cores then this should not take longer
than a month. With systems that scale well to 10 cores I can
equilibrate such a system in under two weeks. Of course, the more
limited your resources are then the more thought that you need to put
into your setup. Very generally, for beginners with at least moderate
computational resources, I suggest immediately following your first
good idea to get the system prepared and then, while it is running,
starting to think about how it could have been done in a better way.
With cpu resources as they are now, your initial run is likely to be
finished faster than anything else if you start it immediately and the
next time you go about this it will be faster because you will figure
out the better method.

Bottom line: an equilibrated bilayer is an equilibrated bilayer, and I
as a reader am not going to have any problem with your final results
even if I think that you could have obtained an equilibrated bilayer
with a quicker method.

Important note: Please use a new subject for a new topic. I know that
topics often diverge, but you started this thread with a vmd-list
question and now you are on to something that is only related to that
by the fact that you study membranes.

Chris.

--- original message ---

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.
Alan Dodd
2008-09-22 08:05:52 UTC
Permalink
(Yes, what Chris Neale said).? I had to do something similar myself, to make a 256-lipid square box from a 128 lipid box.? I used genbox to make a new, larger square box using my original lipid patch as the input file, and then tinkered with the dimensions to get the lipids/leaflet as close to what I wanted as possible, then deleted the excess 1 or 2 lipids in one leaflet.? I wrote a small script to count the lipids in each leaflet, it's not hard to code and I found it immensely useful for generating leaflet-specific index files later.? I must admit, I only actually equilibrated it for 20ns or so.



----- Original Message ----
From: "chris.neale at utoronto.ca" <chris.neale at utoronto.ca>
To: gmx-users at gromacs.org
Sent: Monday, September 22, 2008 6:55:37 AM
Subject: [gmx-users] Leaflet of Bilayer

In my opinion, use any technique that you want (genbox included) then?
run the resulting system for >=50ns while plotting the area per lipid?
and order parameters over time. When these values stop drifting over?
time then you have an equilibrated bilayer. If you have access to a?
cluster that scales well to 4 cores then this should not take longer?
than a month. With systems that scale well to 10 cores I can?
equilibrate such a system in under two weeks. Of course, the more?
limited your resources are then the more thought that you need to put?
into your setup. Very generally, for beginners with at least moderate?
computational resources, I suggest immediately following your first?
good idea to get the system prepared and then, while it is running,?
starting to think about how it could have been done in a better way.?
With cpu resources as they are now, your initial run is likely to be?
finished faster than anything else if you start it immediately and the?
next time you go about this it will be faster because you will figure?
out the better method.

Bottom line: an equilibrated bilayer is an equilibrated bilayer, and I?
as a reader am not going to have any problem with your final results?
even if I think that you could have obtained an equilibrated bilayer?
with a quicker method.

Important note: Please use a new subject for a new topic. I know that?
topics often diverge, but you started this thread with a vmd-list?
question and now you are on to something that is only related to that?
by the fact that you study membranes.

Chris.

--- original message ---

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.

_______________________________________________
gmx-users mailing list? ? gmx-users at gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-request at gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
minnale
2008-09-22 13:05:39 UTC
Permalink
Thanks alot to Chris and Alan for given their valuable suggestions

then a small doubt about time length of bilayer simulation, that is if I concentrate mainly on protein but not on membrane is it require to run >=50ns or 20ns of POPC alone before inserting protein into it.

Earlier I performed only popc simulation for only 5ns then plotted potential energy(it came negative value), average area per lipid(0.64 nm^2/sec). Later protein embedded into 5ns simulated popc bilayer and being run simulations.
What I have done was wrong?
Appreciate for your help
Thanks in advance.
(Yes, what Chris Neale said). I had to do something similar myself, to make a 256-lipid square box from a 128 lipid box. I used genbox to make a new, larger square box using my original lipid patch as the input file, and then tinkered with the dimensions to get the lipids/leaflet as close to what I wanted as possible, then deleted the excess 1 or 2 lipids in one leaflet. I wrote a small script to count the lipids in each leaflet, it's not hard to code and I found it immensely useful for generating leaflet-specific index files later. I must admit, I only actually equilibrated it for 20ns or so.
----- Original Message ----
From: "chris.neale at utoronto.ca" <chris.neale at utoronto.ca>
To: gmx-users at gromacs.org
Sent: Monday, September 22, 2008 6:55:37 AM
Subject: [gmx-users] Leaflet of Bilayer
In my opinion, use any technique that you want (genbox included) then
run the resulting system for >=50ns while plotting the area per lipid
and order parameters over time. When these values stop drifting over
time then you have an equilibrated bilayer. If you have access to a
cluster that scales well to 4 cores then this should not take longer
than a month. With systems that scale well to 10 cores I can
equilibrate such a system in under two weeks. Of course, the more
limited your resources are then the more thought that you need to put
into your setup. Very generally, for beginners with at least moderate
computational resources, I suggest immediately following your first
good idea to get the system prepared and then, while it is running,
starting to think about how it could have been done in a better way.
With cpu resources as they are now, your initial run is likely to be
finished faster than anything else if you start it immediately and the
next time you go about this it will be faster because you will figure
out the better method.
Bottom line: an equilibrated bilayer is an equilibrated bilayer, and I
as a reader am not going to have any problem with your final results
even if I think that you could have obtained an equilibrated bilayer
with a quicker method.
Important note: Please use a new subject for a new topic. I know that
topics often diverge, but you started this thread with a vmd-list
question and now you are on to something that is only related to that
by the fact that you study membranes.
Chris.
--- original message ---
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?
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