Plumed 2.3.2 patching with Gromacs 5.14

[Dharmesh Patel]

Hi I am patching Gromacs 5.1.4 with plumed 2.32. I have installed Plumed in /usr/local path and working fine. But when I aplly patch command in gromacs-5.1.4 directory I am getting error:

[dharmesh@endymion gromacs-5.1.4]$ plumed patch -p
PLUMED patching tool

1) amber14          4) gromacs-5.0.7    7) namd-2.8
2) gromacs-2016.3   5) gromacs-5.1.4    8) namd-2.9
3) gromacs-4.5.7    6) lammps-6Apr13    9) qespresso-5.0.2
Choose the best matching code/version:5
MD engine: gromacs-5.1.4
PLUMED location: /usr/local/lib/plumed
diff file: /usr/local/lib/plumed/patches/gromacs-5.1.4.diff
sourcing config file: /usr/local/lib/plumed/patches/gromacs-5.1.4.config
Executing plumed_before_patch function
PLUMED can be incorporated into gromacs using the standard patching procedure.
Patching must be done in the gromacs root directory  _before_ the cmake command is invoked.

On clusters you may want to patch gromacs using the static version of plumed, in this case
building gromacs can result in multiple errors. One possible solution is to configure gromacs
with these additional options:

cmake -DBUILD_SHARED_LIBS=OFF -DGMX_PREFER_STATIC_LIBS=ON

To enable PLUMED in a gromacs simulation one should use
mdrun with an extra -plumed flag. The flag can be used to
specify the name of the PLUMED input file, e.g.:

gmx mdrun -plumed plumed.dat

This patch also implements the -hrex keyword for gromacs. See \ref hrex

For more information on gromacs you should visit http://www.gromacs.org

Linking Plumed.h and Plumed.inc (shared mode)
Patching with on-the-fly diff from stored originals
/usr/local/lib/plumed/patches/patch.sh: line 261: patch: command not found
/usr/local/lib/plumed/patches/patch.sh: line 261: patch: command not found
/usr/local/lib/plumed/patches/patch.sh: line 261: patch: command not found
/usr/local/lib/plumed/patches/patch.sh: line 261: patch: command not found
/usr/local/lib/plumed/patches/patch.sh: line 261: patch: command not found
/usr/local/lib/plumed/patches/patch.sh: line 261: patch: command not found
/usr/local/lib/plumed/patches/patch.sh: line 261: patch: command not found
/usr/local/lib/plumed/patches/patch.sh: line 261: patch: command not found

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

I would really appreciate your suggestions why I am getting "command not found"

Thanks,

Dharmeshkumar Patel

Research Officer,

Curtin University,

Perth

WA-6152

[Giovanni Bussi]

You should install the "patch" utility. It's a standard unix command

Giovanni

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