[gmx-users] trjconv with or without water?

Thomas Lipscomb linuxborg2 at yahoo.com
Sat Nov 8 23:19:06 CET 2014

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.



"(2) Use trjconv to remove periodicity:
gmx trjconv -s em.tpr -f dppc128.gro -o dppc128_whole.gro -pbc mol -ur compact"

[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

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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
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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

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