[gmx-users] Re: trjconv center problem
ahh, i thought that the program was "skipping" as in not doing the centering command on certain frames due to one reason or another. Ill look into your suggestion Thank you very much for the help. -- View this message in context: http://gromacs.5086.x6.nabble.com/trjconv-center-problem-tp5007473p5007482.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] Re: trjconv center problem
On 4/19/13 4:37 PM, Brad Van Oosten wrote: Ahh, yes perhaps i was unclear. The output file also has the same number of steps. Checking file md50_centered.xtc Reading frame 0 time0.000 # Atoms 27392 Precision 0.001 (nm) Last frame 5 time 10.000 Item#frames Timestep (ps) Step 500012 Time 500012 Lambda 0 Coords 500012 Velocities 0 Forces 0 Box 500012 The simulation is of a pure lipid bilayer, so the result of the centering option is that 99.9% of output frames have the lipid tales centered in the box while the 0.1% of frames seem not to be centered with the water at the center of the box. This is not an issue of skipping frames at all, then. It is an issue of your perception of "center," one that has been discussed many times on this list. This often happens with systems of lipids, multimeric proteins, or receptor-ligand complexes. The "center" of a system is the geometric center, so two molecules together at the visual center of the box and two molecules on opposite "sides" of the box are both considered "centered" since the geometric center of the group coincides with the geometric center of the box. Several iterations of trjconv (including -pbc or -fit options, in separate steps) may be necessary to achieve the desired outcome. http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions#Suggested_trjconv_workflow -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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/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] Re: trjconv center problem
Ahh, yes perhaps i was unclear. The output file also has the same number of steps. Checking file md50_centered.xtc Reading frame 0 time0.000 # Atoms 27392 Precision 0.001 (nm) Last frame 5 time 10.000 Item#frames Timestep (ps) Step 500012 Time 500012 Lambda 0 Coords 500012 Velocities 0 Forces 0 Box 500012 The simulation is of a pure lipid bilayer, so the result of the centering option is that 99.9% of output frames have the lipid tales centered in the box while the 0.1% of frames seem not to be centered with the water at the center of the box. -- View this message in context: http://gromacs.5086.x6.nabble.com/trjconv-center-problem-tp5007473p5007479.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] Re: trjconv center problem
On 4/19/13 4:28 PM, Brad Van Oosten wrote: Checking file md50.xtc Reading frame 0 time0.000 # Atoms 27392 Precision 0.001 (nm) Last frame 5 time 10.000 Item#frames Timestep (ps) Step 500012 Time 500012 Lambda 0 Coords 500012 Velocities 0 Forces 0 Box 500012 Appears to be evenly spaced So then, to clarify, what you're saying is trjconv skips frames when writing output? That was what I was trying to determine from your original post. What does gmxcheck tell you about the output trajectory? -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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/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] Re: trjconv center problem
Checking file md50.xtc Reading frame 0 time0.000 # Atoms 27392 Precision 0.001 (nm) Last frame 5 time 10.000 Item#frames Timestep (ps) Step 500012 Time 500012 Lambda 0 Coords 500012 Velocities 0 Forces 0 Box 500012 Appears to be evenly spaced -- View this message in context: http://gromacs.5086.x6.nabble.com/trjconv-center-problem-tp5007473p5007477.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] Re: trjconv center problem
On 4/19/13 4:19 PM, Brad Van Oosten wrote: The trajectory file is from a consecutive run so i would hope the frames are evenly spaced. What does gmxcheck tell you? No reason to hope when you can prove conclusively one way or another :) -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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/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] Re: trjconv center problem
The trajectory file is from a consecutive run so i would hope the frames are evenly spaced. -- View this message in context: http://gromacs.5086.x6.nabble.com/trjconv-center-problem-tp5007473p5007475.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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
