[gmx-users] problem with gmx solvate

Victor Rosas Garcia rosas.victor at gmail.com
Wed Feb 8 23:48:22 CET 2017

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

I get the following message:

                     :-) GROMACS - gmx solvate, 2016.2 (-:

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    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

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Copyright (c) 2001-2015, The GROMACS development team at
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check out http://www.gromacs.org for more information.

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GROMACS:      gmx solvate, version 2016.2
Executable:   /usr/local/gromacs/bin/gmx
Data prefix:  /usr/local/gromacs
Working dir:  /home/vrosas/2017/11grupoinv/tutorialConservacion/ala10/ALPHA
Command line:
  gmx solvate -cp ../after_em.gro -cs spc216 -o b4em_sol.gro -shell 1.2 -p

Reading solute configuration
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.

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:



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