Re: [gmx-users] Leaflet of Bilayer
(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: "[EMAIL PROTECTED]" <[EMAIL PROTECTED]> To: gmx-users@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@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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[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 listgmx-users@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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Leaflet of Bilayer
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 > > > > > > > > > > > > > > ___ > > gmx-users mailing listgmx-users@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 [EMAIL PROTECTED] > > 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 listgmx-users@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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php 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] title:PhD tel;work:(403) 220-6869 tel;fax:(403) 289-9311 x-mozilla-html:TRUE version:2.1 end:vcard ___ gmx-users mailing listgmx-users@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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Leaflet of Bilayer
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. 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 > > > > > > > > > > > > > > ___ > > gmx-users mailing listgmx-users@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 [EMAIL PROTECTED] > > 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 listgmx-users@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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- 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 ___ gmx-users mailing listgmx-users@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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: Re: [gmx-users] Leaflet of Bilayer
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. 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 > > > > > > > > > > > > > > ___ > > gmx-users mailing listgmx-users@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 [EMAIL PROTECTED] > > 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 listgmx-users@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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Leaflet of Bilayer
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 > > > > > ___ > gmx-users mailing listgmx-users@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 [EMAIL PROTECTED] > 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 listgmx-users@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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Leaflet of Bilayer
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.___ gmx-users mailing listgmx-users@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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
