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Bug #1747

Updated by Mark Abraham over 5 years ago

gromacs 5.0.5 gmx solvate seems to create its own file called temp.top, which causes any existing temp.top to be moved to #temp.top.1# . The original file is not lost, but this is unexpected and (so far as I know) undocumented behaviour. I suggest that if gmx solvate needs to create a temporary .top file then this should ideally be a guaranteed unused filename, or at the very least something much more unlikely to be in use than temp.top. Details from a test demonstration follow.

<pre>
$ ls
empty.gro temp.top waterbox.top

###################

$ cat empty.gro
title
0
5 5 5

###################

$ cat waterbox.top
; Include forcefield parameters
#include "charmm27.ff/forcefield.itp"

; Include water topology
#include "charmm27.ff/tips3p.itp"

#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
; i funct fcx fcy fcz
1 1 1000 1000 1000
#endif

; Include topology for ions
#include "charmm27.ff/ions.itp"

[ system ]
; Name
Gnomes, ROck Monsters And Chili Sauce

[ molecules ]
; Compound #mols

###################

$ gmx solvate -cp empty.gro -cs spc216.gro -p waterbox.top -o waterbox.gro
GROMACS: gmx solvate, VERSION 5.0.5

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 solvate, VERSION 5.0.5
Executable: /project2/p/pomes/cneale/GPC/exe/intel/gromacs-5.0.5/exec_serial/bin/gmx
Library dir: /project2/p/pomes/cneale/GPC/exe/intel/gromacs-5.0.5/exec_serial/share/gromacs/top
Command line:
gmx solvate -cp empty.gro -cs spc216.gro -p waterbox.top -o waterbox.gro

Reading solute configuration
Warning: Number of atoms in empty.gro is 0
title
Containing 0 atoms in 0 residues
Initialising inter-atomic distances...
Note: no atoms in empty.gro
Reading solvent configuration
"216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984"
solvent configuration contains 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 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 --- -------- --------

Will generate new solvent configuration of 3x3x3 boxes
Generating configuration
Sorting configuration
Found 1 molecule type:
SOL ( 3 atoms): 5832 residues
Calculating Overlap...
box_margin = 0.25992
Removed 3393 atoms that were outside the box
Neighborsearching with a cut-off of 0.25992

NOTE: This file uses the deprecated 'group' cutoff_scheme. This will be
removed in a future release when 'verlet' supports all interaction forms.

NOTE: This file uses the deprecated 'group' cutoff_scheme. This will be
removed in a future release when 'verlet' supports all interaction forms.

Table routines are used for coulomb: FALSE
Table routines are used for vdw: FALSE
Cut-off's: NS: 0.25992 Coulomb: 0.25992 LJ: 0.25992
System total charge: 0.000
Potential shift: LJ r^-12: 0.000e+00 r^-6: 0.000e+00, Coulomb 0e+00

Grid: 19 x 19 x 19 cells
Successfully made neighbourlist
nri = 19811, nrj = 130088
Checking Protein-Solvent overlap: tested 0 pairs, removed 0 atoms.
Checking Solvent-Solvent overlap: tested 14524 pairs, removed 1881 atoms.
Added 4074 molecules
Generated solvent containing 12222 atoms in 4074 residues
Writing generated configuration to waterbox.gro

Output configuration contains 12222 atoms in 4074 residues
Volume : 125 (nm^3)
Density : 974.999 (g/l)
Number of SOL molecules: 4074

Processing topology

Back Off! I just backed up temp.top to ./#temp.top.1#
Adding line for 4074 solvent molecules to topology file (waterbox.top)

Back Off! I just backed up waterbox.top to ./#waterbox.top.1#

gcq#6: "It's So Lonely When You Don't Even Know Yourself" (Red Hot Chili Peppers)

###################

Note that temp.top has been backed up by the above command. However, whatever gmx solvate created in temp.top is now gone:

$ ls temp.top
ls: cannot access temp.top: No such file or directory
</pre>


Thank you,
Chris.

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