Set up PLUMED calculations in AMBER20

[Souvik Dey]

Hello,

I am starting to use PLUMED with AMBER20 have no earlier experience of using it. I loaded both the AMBER20 and PLUMED2.5 modules and tried to run a simple metadynamics calculation using the tutorial of Alanine dipeptide from PLUMED website. I have just included the plumed=1 and plumedfile='plumed.dat' into my amber input script, which otherwise runs fine. However, when I try to run the script with PLUMED, I get the following error:

pmemd.cuda.MPI: /software/linux-el7-x86_64/tools/EasyBuild-4.1.0/software/GCCcore/8.3.0/lib64/libgfortran.so.5: version `GFORTRAN_10' not found (required by pmemd.cuda.MPI)
pmemd.cuda.MPI: /software/linux-el7-x86_64/tools/EasyBuild-4.1.0/software/GCCcore/8.3.0/lib64/libgfortran.so.5: version `GFORTRAN_10' not found (required by /software/linux-el7-nvidia/EasyBuild/software/netCDF-Fortran/4.5.3-gompic-2020b/lib/libnetcdff.so.7)

Could someone kindly explain that I I am doing anything wrong here?

Thanks,

Souvik

[Giovanni Bussi]

It looks like you compiled AMBER with gcc/gfortran 10 and plumed with gcc 8.

You can try to set the LD_LIBRARY_PATH so as to point to the gcc 10 libraries, in the hypothesis that a gcc-8-compiled plumed can work linked to gcc 10 libraries. Alternatively, you can recompile plumed with gcc 10.

If this is not possible for some reason, there are slightly more complicated tricks that I can share.

Giovanni

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