[gmx-users] gromacs..
Hello everyone, I am quite new to gromacs. I would like to know how can I calculate the area per lipid for my simulations. I am running simulations with 128 DMPC lipid bilayer. I have the output of 30 ns simulations. Also how can i make a graph with this output. Any help! Henry Biochemistry -- gmx-users mailing listgmx-users@gromacs.org http://lists.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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Two Types of van de Waals interactions in one system
One solution would be to use tabulated potential for which the analytical form does not matter. On Dec 8, 2009, at 4:29 AM, Mark Abraham wrote: hong bingbing wrote: Dear all, Has anyone tried to use 2 van de Waals interaction types in one system? For example, the system includes two components A and B. The van de Waas interaction for A is LJ type, while for B Buckingham form is used. Can GROMACS support two forms simultaneously? No. How would you describe the vdW interaction between an atom from A and one from B? If the reason for this question is based on a desire to mix two force fields - don't. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] xmgrace plot
Hello everyone, I am also new to xmgrace. I have two .xvg file which I have got from the simulation data analysis. How can I open both of them in one xmgrace graph with two distinct color? How can I proceed with the comand? I know this is very basic but I have to learn! Pls give me response. Henry Biochemistry -- gmx-users mailing listgmx-users@gromacs.org http://lists.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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] xmgrace plot
From the command line you can type xmgrace file1.xvg file2.xvg (where file1 and file2 are the filenames!). Jon 2009/12/8 Henry Yang henryy...@yahoo.com Hello everyone, I am also new to xmgrace. I have two .xvg file which I have got from the simulation data analysis. How can I open both of them in one xmgrace graph with two distinct color? How can I proceed with the comand? I know this is very basic but I have to learn! Pls give me response. Henry Biochemistry -- gmx-users mailing listgmx-users@gromacs.org http://lists.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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] xmgrace plot
Hello Jon, Thnx. One more question. I have the output of every 10 ns simulation over 50 ns. For every 10 ns simulation step I have the .xvg file . Is there any way in xmgrace so that I can concatenate all the .xvg file from 0 to 50 ns simulation and show them one xmgrace graph Thanks again Henry From: Jon Fuller jonathan.ful...@gmail.com To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Tue, December 8, 2009 11:53:25 AM Subject: Re: [gmx-users] xmgrace plot From the command line you can type xmgrace file1.xvg file2.xvg (where file1 and file2 are the filenames!). Jon 2009/12/8 Henry Yang henryy...@yahoo.com Hello everyone, I am also new to xmgrace. I have two .xvg file which I have got from the simulation data analysis. How can I open both of them in one xmgrace graph with two distinct color? How can I proceed with the comand? I know this is very basic but I have to learn! Pls give me response. Henry Biochemistry -- gmx-users mailing listgmx-users@gromacs.org http://lists.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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: xmgrace plot
Dear Henry, For Plot two .xgv files u can use following command *xmgrace file1.xvg file2.xvg* colour will come automatically in above case i think file1.xvg will be in BLACK and file2.xvg will be in RED (Its default), You can change aslo. U can add other .xvg file accordingly in above command to get plot for all the .xvg files in a single graph :) Regards Rituraj On Tue, Dec 8, 2009 at 4:30 PM, gmx-users-requ...@gromacs.org wrote: Send gmx-users mailing list submissions to gmx-users@gromacs.org To subscribe or unsubscribe via the World Wide Web, visit http://lists.gromacs.org/mailman/listinfo/gmx-users or, via email, send a message with subject or body 'help' to gmx-users-requ...@gromacs.org You can reach the person managing the list at gmx-users-ow...@gromacs.org When replying, please edit your Subject line so it is more specific than Re: Contents of gmx-users digest... Today's Topics: 1. mpispawn.c:303 Unexpected exit status (shivkumar bale) 2. gromacs.. (Henry Ynag) 3. Re: Two Types of van de Waals interactions in one system (XAvier Periole) 4. xmgrace plot (Henry Yang) 5. Re: xmgrace plot (Jon Fuller) -- Message: 1 Date: Mon, 7 Dec 2009 23:15:44 -0600 From: shivkumar bale kumarb...@gmail.com Subject: [gmx-users] mpispawn.c:303 Unexpected exit status To: gmx-users@gromacs.org Message-ID: 2e20ba9d0912072115idce3ed6w3bfa288eeab1a...@mail.gmail.com Content-Type: text/plain; charset=iso-8859-1 Skipped content of type multipart/alternative-- next part -- A non-text attachment was scrubbed... Name: mdRun300.mdp Type: application/octet-stream Size: 1502 bytes Desc: not available Url : http://lists.gromacs.org/pipermail/gmx-users/attachments/20091207/bba246ab/mdRun300-0001.obj -- Message: 2 Date: Tue, 8 Dec 2009 01:19:16 -0800 (PST) From: Henry Ynag henryy...@yahoo.com Subject: [gmx-users] gromacs.. To: gmx-users@gromacs.org Message-ID: 903781.22164...@web113919.mail.gq1.yahoo.com Content-Type: text/plain; charset=us-ascii Hello everyone, I am quite new to gromacs. I would like to know how can I calculate the area per lipid for my simulations. I am running simulations with 128 DMPC lipid bilayer. I have the output of 30 ns simulations. Also how can i make a graph with this output. Any help! Henry Biochemistry -- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20091208/3059c139/attachment-0001.html -- Message: 3 Date: Tue, 8 Dec 2009 10:52:00 +0100 From: XAvier Periole x.peri...@rug.nl Subject: Re: [gmx-users] Two Types of van de Waals interactions in one system To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 7ecbcabe-b1af-45e5-9723-1d87364fb...@rug.nl Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes One solution would be to use tabulated potential for which the analytical form does not matter. On Dec 8, 2009, at 4:29 AM, Mark Abraham wrote: hong bingbing wrote: Dear all, Has anyone tried to use 2 van de Waals interaction types in one system? For example, the system includes two components A and B. The van de Waas interaction for A is LJ type, while for B Buckingham form is used. Can GROMACS support two forms simultaneously? No. How would you describe the vdW interaction between an atom from A and one from B? If the reason for this question is based on a desire to mix two force fields - don't. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Message: 4 Date: Tue, 8 Dec 2009 02:51:12 -0800 (PST) From: Henry Yang henryy...@yahoo.com Subject: [gmx-users] xmgrace plot To: gromacs gmx-users@gromacs.org Message-ID: 975347.17369...@web113912.mail.gq1.yahoo.com Content-Type: text/plain; charset=us-ascii Hello everyone, I am also new to xmgrace. I have two .xvg file which I have got from the simulation data analysis. How can I open both of them in one xmgrace graph with two distinct color? How can I proceed with the comand? I know this is very basic but I have to learn! Pls give me response. Henry Biochemistry -- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20091208/bcf81b0d/attachment-0001.html -- Message: 5 Date: Tue, 8 Dec 2009 10:53:25 + From
Re: [gmx-users] xmgrace plot
Henry Yang wrote: Hello Jon, Thnx. One more question. I have the output of every 10 ns simulation over 50 ns. For every 10 ns simulation step I have the .xvg file . Is there any way in xmgrace so that I can concatenate all the .xvg file from 0 to 50 ns simulation and show them one xmgrace graph Thanks again It is probably easier to simply concatenate your trajectory files (trjcat) and/or energy files (eneconv) so you don't have to worry about running multiple commands, concatenating all the output of every analysis, and dealing with duplicate start/end times. -Justin Henry *From:* Jon Fuller jonathan.ful...@gmail.com *To:* Discussion list for GROMACS users gmx-users@gromacs.org *Sent:* Tue, December 8, 2009 11:53:25 AM *Subject:* Re: [gmx-users] xmgrace plot From the command line you can type xmgrace file1.xvg file2.xvg (where file1 and file2 are the filenames!). Jon 2009/12/8 Henry Yang henryy...@yahoo.com mailto:henryy...@yahoo.com Hello everyone, I am also new to xmgrace. I have two .xvg file which I have got from the simulation data analysis. How can I open both of them in one xmgrace graph with two distinct color? How can I proceed with the comand? I know this is very basic but I have to learn! Pls give me response. Henry Biochemistry -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.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-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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://lists.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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] gromacs..
Henry Ynag wrote: Hello everyone, I am quite new to gromacs. I would like to know how can I calculate the area per lipid for my simulations. I am running simulations with 128 DMPC lipid bilayer. I have the output of 30 ns simulations. Also how can i make a graph with this output. Plot the relevant box vectors from the .edr file (g_energy). You then have to come up with your own way to multiply these values (to get the total lateral area) and divide by the # of lipids per leaflet. A simple Perl script should do the trick. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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://lists.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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] using trjconv to get a 2x2x2 unit cell for traj.xtc
Dear Jenny, You can do this directly in VMD, using the Periodic tab under Graphics-Representations. Ran Jennifer Williams wrote: Hello, I am trying to find a way around a visualisation problem I am having in VMD. Some of my molecules go over periodic boundary conditions meaning that bonds sometimes appear missing when looking at movies (I am trying to fix this using wrap, unwrap and join in VMD but as yet no luck). I was wondering if there is a way in gromacs to multiply the number of unit cells shown in a trajectory. i.e instead of a 1x1x1 I want the new unit cell to be 2x2x2. This would mean the section of the structure I want to zoom in doesn't go over the pbc. For the confout.gro file I have done this using genconf -nbox 2 2 2 -f confout.gro -o confbig.out and this enables me to at least see a static image where all bonds are present. but in order to view a movie, I need to carry out something similar on the traj.xtc file. I have seen that with trjconv there is the option -box Size for new cubic box but my unit cell is not cubic, it is a parallelepiped. The cell dimensions are : 4.64210 3.77847 1.89596 0.0 0.0 -2.18150 0.0 0.0 0.0 I tried using this anyway with the following command: trjconv -box 9.28414 8.72598 3.79192 -f traj.xtc -o trajbig.xtc but the resulting .xtc file wouldn't load into VMD so I assume that the .xtc file and the .gro file didn't match. Any ideas?, Thanks Jenny --The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. --gmx-users mailing listgmx-users@gromacs.org http://lists.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 thewww interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] using trjconv to get a 2x2x2 unit cell for traj.xtc
Jennifer Williams wrote: Hi Justin Thanks for the suggestions. However, I don't really want to stop the molecule moving into the next image-I start off with an alkyl chain where a large portion of the structure overlaps the pbc. i.e C1-C2-C3 \\ C4-C5-C6 where || is the unit cell boundary. To see the whole alkyl chain I use the graphics/representations/periodic tab in VMD. The problem is that VMD will not allow me to draw a bond between C3 and C4 meaning I get odd looking movies. VMD prefers to join the C3 to the C4 in the same unit cell rather than the C4 sitting right next to it on the other side of the pbc. This means long bonds stretching the length of my unit cell and missing bonds between atoms sitting next to each other! I have spent a while trying to solve this and have posted to the VMD forum (as it is actually a problem with VMD and not gromacs). I still think trjconv -pbc mol would be useful to you. It will make the broken molecules whole, such that they are not split over the periodic boundaries, which seems like it would eliminate your problem. I do the same with lipid bilayers all the time. If I could somehow do the same thing to the traj.xtc as I did to confgro.out using genconf -nbox 2 2 2 that would solve my visualisation problem. Do you know of a way to do this? Even a round-about way? I suppose if I dumped each frame in the trajectory as a pdb, used genbox on them to get a 2x2x2 box and then somehow stuck them together into an .xtc this might work (but any suggestions which are less messy are greatly appreciated!) The only way to do that is indeed the messy way. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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://lists.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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] Re:Re: g_helixorient problem
Command lines that you use? Contents of the index files? Contents of the output files? Catch ya, Dr Dallas Warren Pharmacy and Pharmaceutical Sciences Monash University A polar bear is a Cartesian bear that has undergone a polar transformation -Original Message- From: gmx-users-boun...@gromacs.org on behalf of stefhoor Sent: Wed 12/9/2009 1:44 AM To: gmx-users@gromacs.org Subject: [gmx-users] Re:Re: g_helixorient problem Stefan Hoorman wrote: I am trying to analyse the tilt of my helix with g_helixorient, but all analysis come back as a straight line in 0. I have supplied g_helixorient with the index file containing all carbon alpha atoms of a single helix but simply cannot obtain anything more than this zero line graphic. Some help on the matter would be great. Something's wrong, but we can't possibly tell what without a lot more information. Mark Ok then. My system comprises of a helix of 30 residues inserted into a membrane model DPPC. The protein was inserted aligned to the z axis, which is the normal axis of the membrane. The simulation was carried out for 50ns and the hole system is properly equilibrated. From visual inspection, it is possible to see that the helix is tilted compared to the normal axis. For the g_helixorient analysis, I have created an index file containing all the alpha carbon atoms that constituted my helical domain and analysed the hole trajectory with g_helixorient. The tilt.xvg and also the other outputs all come out as a straight line parallel to x, and 0 in the y axis. If there is any more information please tell me if you need any more information. Thank you winmail.dat-- gmx-users mailing listgmx-users@gromacs.org http://lists.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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Two Types of van de Waals interactions in one system
Yes, you are right! Indeed once I implement the shift scheme in the table, the problem was solved immediately! Thank you so much for your help! Here, I want to include what I did just in case in future, someone has a similar problem: 1. As David said, run a 1 step MD with -debug 1 to generate shifted potential tables: ctab.xvg, dtab.xvg, rtab.xvg; 2. Combine these 3 tables together to become table.xvg: ctab.xvg for electrostatic interaction, dtab.xvg for attraction, rtab.xvg for replusion. You need to change all the sign for the derivative to be the right table format. 3. Now if you use this table as your tabulated potential, the total energy should be conserve in NVE. Thanks, Zhe On Tue, Dec 8, 2009 at 2:32 PM, David van der Spoel sp...@xray.bmc.uu.se wrote: Zhe Wu wrote: Dear David, Thank you so much for your reply! I did try to use nstlist = -1 and I still cannot solve the energy drifting problem. And you can see my problem in more detail from the following link: http://lists.gromacs.org/pipermail/gmx-users/2009-December/047299.html And you mentioned I should use shifted VDW. But in the way I use tabulated potential, the option in vdwtype should be User so that I can indicate I am using a lookup table for the tabulated potential. (In my test case, I used the table provide by GMX 4.0.5 /share/gromacs/top/table6-12.xvg directly, and just changed its name to be table.xvg.) So it seems to me there is no explicit way I can use shift function. Or should I shift the function by changing the potential in the table? Yes you can make a shifted vdw table as well. A simple way to do this is to select vdwtype = shift with the cutoffs of your choice and then run 1 step of MD with the -debug 1 option. Then the tables will be printed into xvg files. Thanks again for your help. Zhe On Tue, Dec 8, 2009 at 1:38 PM, David van der Spoel sp...@xray.bmc.uu.se wrote: Zhe Wu wrote: I agree with that. But I don't know why, when using tabulated potential, I cannot even get a box of LJ particles to have energy conservation in NVE. Anyone has some idea? do you use shifted VdW and nstlist = 1 or nstlist = -1? Zhe On Tue, Dec 8, 2009 at 3:52 AM, XAvier Periole x.peri...@rug.nl wrote: One solution would be to use tabulated potential for which the analytical form does not matter. On Dec 8, 2009, at 4:29 AM, Mark Abraham wrote: hong bingbing wrote: Dear all, Has anyone tried to use 2 van de Waals interaction types in one system? For example, the system includes two components A and B. The van de Waas interaction for A is LJ type, while for B Buckingham form is used. Can GROMACS support two forms simultaneously? No. How would you describe the vdW interaction between an atom from A and one from B? If the reason for this question is based on a desire to mix two force fields - don't. Mark -- gmx-users mailing list gmx-us...@gromacs.org http://lists.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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing list gmx-us...@gromacs.org http://lists.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 thewww interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. David van der Spoel, PhD, Professor of Biology Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 sp...@xray.bmc.uu.se sp...@gromacs.org http://xray.bmc.uu.se/~spoel -- gmx-users mailing list gmx-us...@gromacs.org http://lists.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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. David van der Spoel, PhD, Professor of Biology Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 sp...@xray.bmc.uu.se sp...@gromacs.org http://xray.bmc.uu.se/~spoel -- gmx-users mailing list gmx-us...@gromacs.org
