Re: [gmx-users] g_dist producing inconsistent values
Hi, another quick and dirty tip (but at least it works !) is to generate a new trajectory using trjconv with a huge layer of vacuum on the Z direction (assuming your membrane normal is oriented along Z): you can do that with the -box option with a large value for Z. If you just put only the phosphorous atoms in there this won't generate a large file. Cheers, Patrick Alan Dodd a écrit : - Original Message From: David van der Spoel [EMAIL PROTECTED] To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Thursday, February 7, 2008 6:35:55 PM Subject: Re: [gmx-users] g_dist producing inconsistent values [EMAIL PROTECTED] wrote: I've since found the source of my problem - the program was measuring the (marginally shorter) distance across the PBC boundary, rather than the distance within the box. Unfortunately there doesn't seem to be a way to turn PBC images off (correct me if I'm wrong?), so I guess I'm going to do some jiggerypokery with the data and some math. Distance larger than half a box size are ill-defined anyway in a PBC simulation. -What do you mean? I'd assumed that simply having enough water separating a bilayer from its periodic image that no water 'saw' both bilayers would be sufficient; is this not the case? In some special cases you can do this, for instance within a protein it would work. I've implemented -nopbc options in some programs but not in g_dist yet. Please put it on the developer wishlist. on the wiki. -Done. Until then, I'm using g_traj -ox -com and doing the math with my own script. Many thanks for the various alternative techniques suggested. Never miss a thing. Make Yahoo your home page. http://www.yahoo.com/r/hs ___ 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 -- ___ Patrick FUCHS Equipe de Bioinformatique Genomique et Moleculaire INSERM U726, Universite Paris 7 Case Courrier 7113 2, place Jussieu, 75251 Paris Cedex 05, FRANCE Tel : +33 (0)1-44-27-77-16 - Fax : +33 (0)1-43-26-38-30 E-mail : [EMAIL PROTECTED] Web Site: http://www.ebgm.jussieu.fr/~fuchs ___ 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] g_dist producing inconsistent values
I've since found the source of my problem - the program was measuring the (marginally shorter) distance across the PBC boundary, rather than the distance within the box. Unfortunately there doesn't seem to be a way to turn PBC images off (correct me if I'm wrong?), so I guess I'm going to do some jiggerypokery with the data and some math. Translate some relevant group to the box center with trjconv, and then expand the box size in whatever format you have the structure(s)? Mark ___ 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] g_dist producing inconsistent values
I've since found the source of my problem - the program was measuring the (marginally shorter) distance across the PBC boundary, rather than the distance within the box. Unfortunately there doesn't seem to be a way to turn PBC images off (correct me if I'm wrong?), so I guess I'm going to do some jiggerypokery with the data and some math. Use g_energy to output the box-Z then the distance you want should be the box-Z minus the distance you get. This would be super-dangerous unless you can be sure that it is actually measuring the distance across the boundary each time. If, for instance, it measures the distance you want one time and the distance across the PBC the next time, then Mark's suggestion would be the way to go. Chris. - Original Message I've been using g_dist to plot distances along the normal to my bilayer between groups. Namely in this case, between the phosphates of opposing leaflets, and the peptide. I would expect the sum of the distances between the peptide and each leaflet's phosphates to equal the distance between the two sets of phosphates. But they mysteriously don't. I'm taking the z-distance to be the final value in each row, as the headers in the .xvg indicate: @ s0 legend |d| @ s1 legend d\sx\N @ s2 legend d\sy\N @ s3 legend d\sz\N 0.0003.28371450.0671294 -0.0351439 -3.2828403 The index groups are definitely correct (doublechecked by using trjconv -n -dump and visualising the groups so selected), so there's no error there, I'm sure. And these are the numbers I get out for the first frame: Peptide - leaflet 1 phosphates:-3.3361144 Peptide - leaflet 2 phosphates:0.2953452 Leaflet 1 - leaflet 2 phosphates:-3.2828403 Is there an error in my understanding of how this is working? I'm pretty certain the first two numbers should sum to the value of the third number. Alternatively, any idea what could be going wrong? The files being used are definitely the same, too... Alan. ___ 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] g_dist producing inconsistent values
- Original Message From: David van der Spoel [EMAIL PROTECTED] To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Thursday, February 7, 2008 6:35:55 PM Subject: Re: [gmx-users] g_dist producing inconsistent values [EMAIL PROTECTED] wrote: I've since found the source of my problem - the program was measuring the (marginally shorter) distance across the PBC boundary, rather than the distance within the box. Unfortunately there doesn't seem to be a way to turn PBC images off (correct me if I'm wrong?), so I guess I'm going to do some jiggerypokery with the data and some math. Distance larger than half a box size are ill-defined anyway in a PBC simulation. -What do you mean? I'd assumed that simply having enough water separating a bilayer from its periodic image that no water 'saw' both bilayers would be sufficient; is this not the case? In some special cases you can do this, for instance within a protein it would work. I've implemented -nopbc options in some programs but not in g_dist yet. Please put it on the developer wishlist. on the wiki. -Done. Until then, I'm using g_traj -ox -com and doing the math with my own script. Many thanks for the various alternative techniques suggested. Never miss a thing. Make Yahoo your home page. http://www.yahoo.com/r/hs ___ 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] g_dist producing inconsistent values
[EMAIL PROTECTED] wrote: I've since found the source of my problem - the program was measuring the (marginally shorter) distance across the PBC boundary, rather than the distance within the box. Unfortunately there doesn't seem to be a way to turn PBC images off (correct me if I'm wrong?), so I guess I'm going to do some jiggerypokery with the data and some math. Distance larger than half a box size are ill-defined anyway in a PBC simulation. In some special cases you can do this, for instance within a protein it would work. I've implemented -nopbc options in some programs but not in g_dist yet. Please put it on the developer wishlist. on the wiki. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David van der Spoel, Ph.D. Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ 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] g_dist producing inconsistent values
I've been using g_dist to plot distances along the normal to my bilayer between groups. Namely in this case, between the phosphates of opposing leaflets, and the peptide. I would expect the sum of the distances between the peptide and each leaflet's phosphates to equal the distance between the two sets of phosphates. But they mysteriously don't. I'm taking the z-distance to be the final value in each row, as the headers in the .xvg indicate: @ s0 legend |d| @ s1 legend d\sx\N @ s2 legend d\sy\N @ s3 legend d\sz\N 0.0003.28371450.0671294 -0.0351439 -3.2828403 The index groups are definitely correct (doublechecked by using trjconv -n -dump and visualising the groups so selected), so there's no error there, I'm sure. And these are the numbers I get out for the first frame: Peptide - leaflet 1 phosphates:-3.3361144 Peptide - leaflet 2 phosphates:0.2953452 Leaflet 1 - leaflet 2 phosphates:-3.2828403 Is there an error in my understanding of how this is working? I'm pretty certain the first two numbers should sum to the value of the third number. Alternatively, any idea what could be going wrong? The files being used are definitely the same, too... Alan. Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now. http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ ___ 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
