Re: [gmx-users] using trjconv to get a 2x2x2 unit cell for traj.xtc
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). 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!) Jenny Quoting "Justin A. Lemkul" : 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. Correcting periodicity should alleviate some of the problems. Using trjconv -pbc mol (or -pbc nojump) is typically the best first step. -Justin Any ideas?, Thanks Jenny -- 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 Dr. Jennifer Williams Institute for Materials and Processes School of Engineering University of Edinburgh Sanderson Building The King's Buildings Mayfield Road Edinburgh, EH9 3JL, United Kingdom Phone: ++44 (0)131 650 4 861 -- 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 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] 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: 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. Correcting periodicity should alleviate some of the problems. Using trjconv -pbc mol (or -pbc nojump) is typically the best first step. -Justin Any ideas?, Thanks Jenny -- 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
[gmx-users] using trjconv to get a 2x2x2 unit cell for traj.xtc
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 the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
