Justin, I've used trjconv -pbc mol -ur compact but the final picture was still wrong :(
So I think that something happened with my box because 1- If the cubic representation is set on default why other .gro structures were visualized in VMD in dodecahedral box on default ? 2- Why the pereodic boundaries were distorded in the next stage after NPT (production MD) that my structure were outside the box on half ? I want to point that on MD stage the box were dodecahedral again like in the NVT and other stages but my structure was in wrong position. James 2011/10/24 Justin A. Lemkul <jalem...@vt.edu> > > > James Starlight wrote: > >> Justin, hello! >> >> >> I have forced with some problem during final stage of your turorial. >> >> I dont know why but after NPT phase my sytem has occured in the standart >> cubic box instead of dodecahedron (after all previosly phases my system was >> in correct box). >> >> So when I've passed my system in the MD stage- it's moved back into normal >> dodecahedron box but on the placement where previously system was. So as the >> consequence I've obtained protein in the wrong place ( some of its parts >> were outside new box ) >> >> I've tried examined why this might occur but have not found possible >> explanations. >> >> I've examined box coordinates of the all .gro structurs obtained after >> each of the stages and all of them contained such box vectors >> 7.85059 7.85059 5.55120 0.00000 0.00000 0.00000 0.00000 >> 3.92529 3.92529 >> >> As I understood It's correspond to the system in the dodecahedron box but >> my ntp.gro structure with the same is in the cubic box ( with the above box >> coordinates as well). Why its might occured and were else information of the >> box coordinates is present exept of initial structure gro file ? >> >> > You still have a dodecahedral box. The default representation is a simple > triclinic cell. A true compact representation can be obtained with: > > trjconv -pbc mol -ur compact > > -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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==============================**========== > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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<http://www.gromacs.org/Support/Mailing_Lists> >
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