[gmx-users] trjconv not able to generated output

[Sergio Manzetti]

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 

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From: "Justin Lemkul" <jalemkul at vt.edu> 
To: "gmx-users" <gmx-users at 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 at 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 

-- 
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Justin A. Lemkul, Ph.D. 
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Virginia Tech Department of Biochemistry 

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