Re: [gmx-users] How to apply trjconv -nojump to a part of a system
On 7/9/13 7:13 PM, Bin Liu wrote: Hi All, For the convenience of visualization, I need to remove the jump of one component (say a protein) of the system at the boundary. I don't need to, or say I need not to remove the jump of the other components (say a lipid bilayer), since otherwise the system will look falling apart. I noticed I can cluster a part of a system, then output all the atoms in the system in which only the part is clustered, and the other components unchanged. Does GROMACS have similar function when *-nojump* is used? If this can not be accomplished directly, is there a way to circumvent it? I figured out a way, but haven't implemented it. I can plug the coordinates of the protein treated with *-nojump* into the trajectory of the whole system which is not treated with *-nojump*. It is kind of substituting the coordinates of one component in one trajectory with the coordinates of the same component in another trajectory. Is there anyone aware of a tool or a script to do this job? Would this actually work? I would think the protein would collide with other elements of the system - solvent, etc. Wouldn't fitting be a better option here? If the protein moves in relation to a surface, something like trjconv -fit transxy is probably quite useful. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Associate Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] How to apply trjconv -nojump to a part of a system
VMD might do what you want with the PBC tools plugin (installed by default). http://www.ks.uiuc.edu/Research/vmd/plugins/pbctools/ unwrap being the equivalent of -nojump Otherwise, couldn't you just view your 2 trajectories simultaneously, one with protein the other not? -Trayder On Wed, Jul 10, 2013 at 9:13 AM, Bin Liu fdusuperstr...@gmail.com wrote: Hi All, For the convenience of visualization, I need to remove the jump of one component (say a protein) of the system at the boundary. I don't need to, or say I need not to remove the jump of the other components (say a lipid bilayer), since otherwise the system will look falling apart. I noticed I can cluster a part of a system, then output all the atoms in the system in which only the part is clustered, and the other components unchanged. Does GROMACS have similar function when *-nojump* is used? If this can not be accomplished directly, is there a way to circumvent it? I figured out a way, but haven't implemented it. I can plug the coordinates of the protein treated with *-nojump* into the trajectory of the whole system which is not treated with *-nojump*. It is kind of substituting the coordinates of one component in one trajectory with the coordinates of the same component in another trajectory. Is there anyone aware of a tool or a script to do this job? Thank you very much. Regards Bin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
RE: [gmx-users] How to apply trjconv -nojump to a part of a system
Thanks mate, I am trying it now :) -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Trayder Thomas Sent: Thursday, 11 July 2013 11:52 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] How to apply trjconv -nojump to a part of a system VMD might do what you want with the PBC tools plugin (installed by default). http://www.ks.uiuc.edu/Research/vmd/plugins/pbctools/ unwrap being the equivalent of -nojump Otherwise, couldn't you just view your 2 trajectories simultaneously, one with protein the other not? -Trayder On Wed, Jul 10, 2013 at 9:13 AM, Bin Liu fdusuperstr...@gmail.com wrote: Hi All, For the convenience of visualization, I need to remove the jump of one component (say a protein) of the system at the boundary. I don't need to, or say I need not to remove the jump of the other components (say a lipid bilayer), since otherwise the system will look falling apart. I noticed I can cluster a part of a system, then output all the atoms in the system in which only the part is clustered, and the other components unchanged. Does GROMACS have similar function when *-nojump* is used? If this can not be accomplished directly, is there a way to circumvent it? I figured out a way, but haven't implemented it. I can plug the coordinates of the protein treated with *-nojump* into the trajectory of the whole system which is not treated with *-nojump*. It is kind of substituting the coordinates of one component in one trajectory with the coordinates of the same component in another trajectory. Is there anyone aware of a tool or a script to do this job? Thank you very much. Regards Bin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] How to apply trjconv -nojump to a part of a system
Hi All, For the convenience of visualization, I need to remove the jump of one component (say a protein) of the system at the boundary. I don't need to, or say I need not to remove the jump of the other components (say a lipid bilayer), since otherwise the system will look falling apart. I noticed I can cluster a part of a system, then output all the atoms in the system in which only the part is clustered, and the other components unchanged. Does GROMACS have similar function when *-nojump* is used? If this can not be accomplished directly, is there a way to circumvent it? I figured out a way, but haven't implemented it. I can plug the coordinates of the protein treated with *-nojump* into the trajectory of the whole system which is not treated with *-nojump*. It is kind of substituting the coordinates of one component in one trajectory with the coordinates of the same component in another trajectory. Is there anyone aware of a tool or a script to do this job? Thank you very much. Regards Bin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
