[gmx-users] trjconv with or without water?

Justin Lemkul jalemkul at vt.edu
Sat Nov 8 23:28:36 CET 2014

On 11/8/14 5:19 PM, Thomas Lipscomb wrote:
> Dear gmx-users,
> I am following the tutorial below but it doesn't mention choosing a group (see command line dump below, I have to choose between 0 and 5).  I am trying to insert a small protein into a membrane so I think I should choose 0 or 5 depending on whether I should keep the water molecules.  I mean maybe I should remove the water and choose 5 because I am inserting the protein into the membrane and the water molecules around the protein would get in the way?  I want to simulate the membrane with water molecules around it, though.

In this case, the choice of output is largely irrelevant.  The subsequent 
construction steps will remove water either way.


> Thanks.
> Sincerely,
> Thomas
> "(2) Use trjconv to remove periodicity:
> gmx trjconv -s em.tpr -f dppc128.gro -o dppc128_whole.gro -pbc mol -ur compact"
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/03_solvate.html
> [tlipscomb at prime-radiant KALP]$ /usr/local/gromacs/bin/gmx trjconv -s em.tpr -f dppc128.gro -o dppc128_whole.gro -pbc mol -ur compact
> GROMACS:    gmx trjconv, VERSION 5.0.1
> 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 Peter Kasson       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     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) 2001-2014, 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 5.0.1
> Executable:   /usr/local/gromacs/bin/gmx
> Library dir:  /usr/local/gromacs/share/gromacs/top
> Command line:
>    gmx trjconv -s em.tpr -f dppc128.gro -o dppc128_whole.gro -pbc mol -ur compact
> Will write gro: Coordinate file in Gromos-87 format
> Reading file em.tpr, VERSION 5.0.1 (single precision)
> Reading file em.tpr, VERSION 5.0.1 (single precision)
> Select group for output
> Group     0 (         System) has 17365 elements
> Group     1 (          Other) has  6400 elements
> Group     2 (           DPPC) has  6400 elements
> Group     3 (          Water) has 10965 elements
> Group     4 (            SOL) has 10965 elements
> Group     5 (      non-Water) has  6400 elements


Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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