Dear all,
Thank you for your help.
Here is a summary of the replies received:
---> Neli Fonseca, EBI, suggested the use of Docker containers,
"
https://hub.docker.com/search?q=gromacs&type=image
https://hub.docker.com/search?q=cp2k&type=image
https://hub.docker.com/search?q=nwchem&type=image "
---> Jeroen Mesters, Biochem Uni Lubeck and later Amit Singh pointed at
the pkgs page for gromacs (Centos 7):
https://centos.pkgs.org/7/epel-x86_64/gromacs-2018.8-1.el7.x86_64.rpm.html
It then became clear why my attempt at "yum install gromacs" followed by
"which gromacs" returned an error message (the command is "gmx");
---> Chris Roome, mpimf-heidelberg:
"If you're insterested, recently compiled the latest Gromacs 2020, seems
to work fine.
I compiled GCC v5.5.0 first, and set the LD... and exe path (your path
will differ of course) here's mine, with tcsh:
setenv LD_LIBRARY_PATH /software/gcc-5/lib64
set path = ( /software/gcc-5/bin $path )
As you say, even with this, cmake picks up the old, system installed
gcc, so I had to specify on the cmake cmd:
cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON
-DCMAKE_C_COMPILER=gcc -DCMAKE_CXX_COMPILER=c++ -DGMX_MPI=on
-DCMAKE_INSTALL_PREFIX=/software/gromacs-2020 -DREGRESSIONTEST_DOWNLOAD
since cmake picks up the old cc even with the correct paths.
I installed the MPI version, so if you want that, you'll need to install
the openmpi and openmpi-devel packages with yum. Then do a 'module load
mpi' before the cmake."
---> Abhik Mukhopadhyay suggested the use of NAMD,
https://www.ks.uiuc.edu/Research/namd/
---> Eugene Osipov: you can try NAMD, Amber (cost-free CPU-only academic
version) or Desmond - their installation is simple and they work
reasonably well.
---> Jack Tanner (U. Missouri-Columbia): "You might want to review the
literature on using MD to study diffusion of O2/CO in myoglobin." (I had
started in fact)
[---> Lorenzo Briganti: the reply seems to have been lost along the way].
Hoping this will be useful to others, and thank you once again.
Fred. Vellieux, 1st Faculty of Medicine, Charles University in Prague,
BIOCEV Vestec site
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