I have done this many times before, its doesn't give any problems, it gives the last frame and only that. But not in this case
Sergio Manzetti [ http://www.fjordforsk.no/logo_hr2.jpg ] [ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ | ] Midtun 6894 Vangsnes Norge Org.nr. 911 659 654 Tlf: +47 57695621 [ http://www.oekolab.com/ | Økolab ] | [ http://www.nanofact.no/ | Nanofactory ] | [ http://www.aq-lab.no/ | AQ-Lab ] | [ http://www.phap.no/ | FAP ] From: "Justin Lemkul" <jalem...@vt.edu> To: "gmx-users" <gmx-us...@gromacs.org> Sent: Friday, September 8, 2017 3:52:52 PM Subject: Re: [gmx-users] trjconv not able to generated output On 9/8/17 9:38 AM, Sergio Manzetti wrote: > Hi, I have tried several ways to get the last frame from the output xtc using > gmx trjconv, like: > > sem@Fjordforsk:/media/sem/HDD3/files/sims/BPRP/5$ gmx trjconv -f traj_c -o > confout.gro -b 2000 -e 2000 > :-) GROMACS - gmx trjconv, VERSION 5.1.2 (-: > > GROMACS is written by: > Emile Apol Rossen Apostolov Herman J.C. Berendsen Par Bjelkmar > Aldert van Buuren Rudi van Drunen Anton Feenstra Sebastian Fritsch > Gerrit Groenhof Christoph Junghans Anca Hamuraru Vincent Hindriksen > Dimitrios Karkoulis Peter Kasson Jiri Kraus Carsten Kutzner > Per Larsson Justin A. Lemkul Magnus Lundborg Pieter Meulenhoff > Erik Marklund Teemu Murtola Szilard Pall Sander Pronk > Roland Schulz Alexey Shvetsov Michael Shirts Alfons Sijbers > Peter Tieleman Teemu Virolainen Christian Wennberg Maarten Wolf > and the project leaders: > Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel > > Copyright (c) 1991-2000, University of Groningen, The Netherlands. > Copyright (c) 2001-2015, The GROMACS development team at > Uppsala University, Stockholm University and > the Royal Institute of Technology, Sweden. > check out http://www.gromacs.org for more information. > > GROMACS is free software; you can redistribute it and/or modify it > under the terms of the GNU Lesser General Public License > as published by the Free Software Foundation; either version 2.1 > of the License, or (at your option) any later version. > > GROMACS: gmx trjconv, VERSION 5.1.2 > Executable: /usr/bin/gmx > Data prefix: /usr > Command line: > gmx trjconv -f traj_c -o confout.gro -b 2000 -e 2000 > > Will write gro: Coordinate file in Gromos-87 format > Reading file topol.tpr, VERSION 5.1.2 (single precision) > Reading file topol.tpr, VERSION 5.1.2 (single precision) > Select group for output > Group 0 ( System) has 50510 elements > Group 1 ( DNA) has 1333 elements > Group 2 ( NA) has 71 elements > Group 3 ( CL) has 31 elements > Group 4 ( PRB) has 28 elements > Group 5 ( Ion) has 102 elements > Group 6 ( NA) has 71 elements > Group 7 ( CL) has 31 elements > Group 8 ( PRB) has 28 elements > Group 9 ( Other) has 28 elements > Group 10 ( NA) has 71 elements > Group 11 ( CL) has 31 elements > Group 12 ( PRB) has 28 elements > Group 13 ( Water) has 49047 elements > Group 14 ( SOL) has 49047 elements > Group 15 ( non-Water) has 1463 elements > Group 16 ( Water_and_ions) has 49149 elements > Select a group: 15 > Selected 15: 'non-Water' > Reading frame 0 time 2000.000 > Precision of traj_c.xtc is 0.001 (nm) > Using output precision of 0.001 (nm) > > Back Off! I just backed up confout.gro to ./#confout.gro.1# > Last frame 0 time 2000.000 > > however, something is wrong with the trajectory, even tried the xtc, same > problem there. There seems to be enough frames, but they don't "appear" after > the selection of groups. You're telling trjconv to skip everything before 2000 ps with -b 2000, so the program will not report any reading of frames before that time. If there was actually a problem, the program would crash with a fatal error. > How can I repair or check a trajectory? gmx check, and it will surely report that everything is fine. -Justin -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.biochem.vt.edu/people/faculty/JustinLemkul.html ================================================== -- 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.
