[gmx-users] The octahedron problem
Dear Gromacs Users, I have the problem with generating the octahedron box. I always get the rectangular box (using VMD) When I searched on the gmx maillist, I saw some people met same problem. Is problem is normal in gromacs? After run simulation, I can display the trajectory on VMD by using the command trjconv -pbc mol -ur compact for converting the system. But I can not display the octahedron box after solvated system. Could someone help me ? Tuong Vy -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] The octahedron problem
Hi Tuong Vy, An octahedral or dodecahedral box is pretty tricky. I have a Pymol script for generating them, but it will probably require some more work... Cheers, Tsjerk On May 19, 2015 13:18, "Vy Phan" wrote: > Dear Gromacs Users, > I have the problem with generating the octahedron box. I always get the > rectangular box (using VMD) > When I searched on the gmx maillist, I saw some people met same problem. > Is problem is normal in gromacs? > > After run simulation, I can display the trajectory on VMD by using the > command trjconv -pbc mol -ur compact for converting the system. But I can > not display the octahedron box after solvated system. > > Could someone help me ? > > Tuong Vy > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] The octahedron problem
>I have the problem with generating the octahedron box. I always get the rectangular box (using VMD) That's normal and not a problem: "any periodic cell shape can be expressed as a parallelepiped (a.k.a. triclinic cell), and GROMACS does so internally regardless of the initial shape of the box." http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions -- James "Wes" Barnett Ph.D. Candidate Chemical and Biomolecular Engineering Tulane University Boggs Center for Energy and Biotechnology, Room 341-B New Orleans, Louisiana 70118 jbarn...@tulane.edu LinkedIn From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Vy Phan Sent: Tuesday, May 19, 2015 6:18 AM To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: [gmx-users] The octahedron problem Dear Gromacs Users, I have the problem with generating the octahedron box. I always get the rectangular box (using VMD) When I searched on the gmx maillist, I saw some people met same problem. Is problem is normal in gromacs? After run simulation, I can display the trajectory on VMD by using the command trjconv -pbc mol -ur compact for converting the system. But I can not display the octahedron box after solvated system. Could someone help me ? Tuong Vy -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] The octahedron problem
Dear Tsjerk Wassenaar Can I display it on the VMD ? Thank a lot Tuong Vy 2015-05-19 20:22 GMT+09:00 Tsjerk Wassenaar : > Hi Tuong Vy, > > An octahedral or dodecahedral box is pretty tricky. I have a Pymol script > for generating them, but it will probably require some more work... > > Cheers, > > Tsjerk > On May 19, 2015 13:18, "Vy Phan" wrote: > > > Dear Gromacs Users, > > I have the problem with generating the octahedron box. I always get the > > rectangular box (using VMD) > > When I searched on the gmx maillist, I saw some people met same problem. > > Is problem is normal in gromacs? > > > > After run simulation, I can display the trajectory on VMD by using the > > command trjconv -pbc mol -ur compact for converting the system. But I can > > not display the octahedron box after solvated system. > > > > Could someone help me ? > > > > Tuong Vy > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] The octahedron problem
Hi Tuong Vy, No, it uses Pymol CGO to draw the cell. I think that won't work in VMD. Cheers, Tsjerk On May 19, 2015 15:28, "Vy Phan" wrote: > Dear Tsjerk Wassenaar > Can I display it on the VMD ? > Thank a lot > Tuong Vy > > 2015-05-19 20:22 GMT+09:00 Tsjerk Wassenaar : > > > Hi Tuong Vy, > > > > An octahedral or dodecahedral box is pretty tricky. I have a Pymol script > > for generating them, but it will probably require some more work... > > > > Cheers, > > > > Tsjerk > > On May 19, 2015 13:18, "Vy Phan" wrote: > > > > > Dear Gromacs Users, > > > I have the problem with generating the octahedron box. I always get > the > > > rectangular box (using VMD) > > > When I searched on the gmx maillist, I saw some people met same > problem. > > > Is problem is normal in gromacs? > > > > > > After run simulation, I can display the trajectory on VMD by using the > > > command trjconv -pbc mol -ur compact for converting the system. But I > can > > > not display the octahedron box after solvated system. > > > > > > Could someone help me ? > > > > > > Tuong Vy > > > -- > > > Gromacs Users mailing list > > > > > > * Please search the archive at > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > > posting! > > > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > * For (un)subscribe requests visit > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > > send a mail to gmx-users-requ...@gromacs.org. > > > > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
