patching gromacs with Plumed

[Estelina Silva]

Hello

I have successfully compiled plumed on my machine, which I will be accessing through ssh for the tutorial with my laptop. However, I am having problems patching Plumed with gromacs (which I am compiling for the tutorial has well).

By following your instructions closely on github and, for plumed, every check command seems to work out fine.
However, for Gromacs and by following the patch command:

plumed patch -p --runtime -e gromacs-5.1.4


I get the following error message:

MD engine: gromacs-5.1.4
PLUMED location: /home/elora/plumed2/
diff file: /home/elora/plumed2//patches/gromacs-5.1.4.diff
sourcing config file: /home/elora/plumed2//patches/gromacs-5.1.4.config
ERROR: Preliminary test not passed.
It seems that this is not gromacs-5.1.4, or you are in the wrong directory
If you are sure about what you are doing, use -f

If including -f in the command line, the patch command runs and when checking the content in the build directory I find that three links are created, namely:

Plumed.cmake  Plumed.h  Plumed.inc

However I do get the following error message:

Linking Plumed.h and Plumed.inc (runtime mode)
Patching with on-the-fly diff from stored originals
ERROR: File ./src/gromacs/CMakeLists.txt is missing
ERROR: File ./src/gromacs/mdlib/force.cpp is missing
ERROR: File ./src/gromacs/mdlib/minimize.cpp is missing
ERROR: File ./src/programs/mdrun/md.cpp is missing
ERROR: File ./src/programs/mdrun/mdrun.cpp is missing
ERROR: File ./src/programs/mdrun/repl_ex.cpp is missing
ERROR: File ./src/programs/mdrun/repl_ex.h is missing
ERROR: File ./src/programs/mdrun/runner.cpp is missing

You are patching in runtime mode
Be warned that when you will run MD you will use the PLUMED version pointed at
by the PLUMED_KERNEL environment variable

PLUMED is compiled with MPI support so you can configure gromacs-5.1.4 with MPI

When checking the src directory the mentioned files are there, so not sure what the complaint is about...

Also I have tried to change the command line with the following options because of the error message:

patch -p --runtime -d $HOME/plumed2/patches/  -e gromacs-5.1.4

But again resulting in error messages about the sourcing config files:

sourcing config file: /home/elora/plumed2//patches/gromacs-5.1.4.config
ERROR: Preliminary test not passed.
It seems that this is not gromacs-5.1.4, or you are in the wrong directory

Inspite this and when configuring and compiling gromacs, the code seems to compile without error messages. But, when typing the suggested command line

gmx_mpi mdrun -h | grep plumed

I do not get the message stated on github, but I get the following:

 gmx_mpi mdrun -h | grep plumed
                   :-) GROMACS - gmx mdrun, VERSION 5.1.4 (-:

                            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   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 mdrun, VERSION 5.1.4
Executable:   /usr/local/bin/gmx_mpi
Data prefix:  /usr/local
Command line:
  gmx_mpi mdrun -h

I assume with this that gromacs is still not patched with Plumed...Any help regarding this issue is most welcome.

Kind Regards!
Estelina Silva
University of Aveiro

[Giovanni Bussi]

Hi,

I think there is a mistake in the instructions, I will fix it right now. To be precise, this:

wget ftp://ftp.gromacs.org/pub/gromacs/gromacs-5.1.4.tar.gz

tar xzf gromacs-5.1.4.tar.gz

cd gromacs-5.1.4

mkdir build

plumed patch -p --runtime -e gromacs-5.1.4

cd build

Should be instead this:

wget ftp://ftp.gromacs.org/pub/gromacs/gromacs-5.1.4.tar.gz

tar xzf gromacs-5.1.4.tar.gz

cd gromacs-5.1.4

mkdir build

plumed patch -p --runtime -e gromacs-5.1.4

cd build

That is "plumed patch" command should be executed from gromacs-5.1.4 directory. Sorry for that!

Giovanni

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