[gmx-users] problem with gmx solvate

Thu Feb 9 14:15:37 CET 2017

Wow. My first bug uncovered in GROMACS.

Thanks.

Victor

2017-02-09 0:16 GMT-06:00 David van der Spoel <spoel at xray.bmc.uu.se>:

> On 08/02/17 23:48, Victor Rosas Garcia wrote:
>
>> Hello everybody,
>>
>> I am having problems with gmx solvate.  I am trying to solvate a small
>> peptide with a solvent shell 1.2 nm thick.  When I use the following
>> command line:
>>
>> gmx solvate -cp ../after_em.gro -cs spc216 -o b4em_sol.gro -shell 1.2 -p
>> ../topol.top
>>
>> I get the following message:
>>
>>                      :-) GROMACS - gmx solvate, 2016.2 (-:
>>
>>                             GROMACS is written by:
>>      Emile Apol      Rossen Apostolov  Herman J.C. Berendsen    Par
>> Bjelkmar
>>  Aldert van Buuren   Rudi van Drunen     Anton Feenstra    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 solvate, version 2016.2
>> Executable:   /usr/local/gromacs/bin/gmx
>> Data prefix:  /usr/local/gromacs
>> Working dir:  /home/vrosas/2017/11grupoinv/t
>> utorialConservacion/ala10/ALPHA
>> Command line:
>>   gmx solvate -cp ../after_em.gro -cs spc216 -o b4em_sol.gro -shell 1.2 -p
>> ../topol.top
>>
>> Reading solute configuration
>> Protein
>> Containing 112 atoms in 12 residues
>> Reading solvent configuration
>> 216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984
>> Containing 648 atoms in 216 residues
>>
>> Initialising inter-atomic distances...
>>
>> WARNING: Masses and atomic (Van der Waals) radii will be guessed
>>          based on residue and atom names, since they could not be
>>          definitively assigned from the information in your input
>>          files. These guessed numbers might deviate from the mass
>>          and radius of the atom type. Please check the output
>>          files if necessary.
>>
>> NOTE: From version 5.0 gmx solvate uses the Van der Waals radii
>> from the source below. This means the results may be different
>> compared to previous GROMACS versions.
>>
>> ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
>> A. Bondi
>> van der Waals Volumes and Radii
>> J. Phys. Chem. 68 (1964) pp. 441-451
>> -------- -------- --- Thank You --- -------- --------
>>
>> Generating solvent configuration
>> Will generate new solvent configuration of 4x4x4 boxes
>> Solvent box contains 25131 atoms in 8377 residues
>> Removed 4044 solvent atoms due to solvent-solvent overlap
>> Removed 21087 solvent atoms due to solute-solvent overlap
>> Sorting configuration
>> Found 0 different molecule types:
>> Generated solvent containing 0 atoms in 0 residues
>> Writing generated configuration to b4em_sol.gro
>>
>> Back Off! I just backed up b4em_sol.gro to ./#b4em_sol.gro.8#
>>
>> Output configuration contains 112 atoms in 12 residues
>> Volume                 :         216 (nm^3)
>> Density                :      6.4369 (g/l)
>> Number of SOL molecules:      0
>>
>> Processing topology
>>
>> Back Off! I just backed up ../topol.top to ../#topol.top.8#
>>
>> GROMACS reminds you: "Keep Your Shoes and Socks On, People" (F. Zappa)
>>
>>
>> indicating zero solvent molecules were added.  Am I doing something wrong
>> with the gmx solvent options?
>>
>> the gro and the top files I am using can be found at:
>> https://www.dropbox.com/s/wjtfoj6c2sufv14/after_em.gro?dl=0
>> https://www.dropbox.com/s/n02pw7bel4qwe4l/topol.top?dl=0
>>
>> Regards
>>
>> Victor
>>
>> Apparently the -shell option does something fishy. Removing it makes the
> program work. Unless you want a spherical shell around your program you
> should not use the -shell option. Nevertheless I put in a bug report:
>
> https://redmine.gromacs.org/issues/2119
>
> --
> David van der Spoel, Ph.D., Professor of Biology
> Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
> spoel at xray.bmc.uu.se    http://folding.bmc.uu.se
> --
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