Hello,
While going through the bAIes tutorial I encountered the following few errors.
The bAIes installation does not specify installing several python and lammps packages:
Following are some additional packages that I needed to install:
-
Install additional python packages: pip install matplotlib scipy lmfit
-
Install additional LAMMPS packages
cmake -D PKG_MOLECULE=ON ../cmake
cmake -D PKG_EXTRA-FIX=ON ../cmake
make -j 10
make install
- Install BLAS (Basic Linear Algebra Subprogram)
sudo yum install blas-devel lapack-devel
- Install PLUMEd after BLAS
cmake -D PKG_PLUMED=ON ../cmake
In tutorial/bAIes/ Step 4:
The directory tutorial/bAIes/4-simulation/
Contains cmap_20240524.cmap, however idp_nvt.in requires dry_ff_20240524_correct.cmap
Error: ERROR on proc 0: cannot open cmap grid potential file dry_ff_20240524_correct.cmap: No such file or directory (src/potential_file_reader.cpp:59)
Changing dry_ff_20240524_correct.cmap to Contains cmap_20240524.cmap resolves the error.
Further, the directory contains `plumed.dat` file, however `idp_nvt.in` requires `plumed_idp.dat`. Are these files the same?
After changing the filename to `plumed.dat` in `idp_nvt.in` script, I get the following error:
`Error: I cannot understand line: BAIES LABEL=baies ATOMS=batoms DATA_FILE=baies_params.dat PRIOR=JEFFREYS TEMP=2.478541306`
I also have a few queries regarding the input files:
- .pdb and .gro files output by pdb2gmx do not contain TER betwen multiple chains. Is that a problem?
- Does the
cmap_20240524.cmap remain constant for all systems?
Thanks
Kartik
Hello,
While going through the bAIes tutorial I encountered the following few errors.
The bAIes installation does not specify installing several python and lammps packages:
Following are some additional packages that I needed to install:
Install additional python packages:
pip install matplotlib scipy lmfitInstall additional LAMMPS packages
In
tutorial/bAIes/Step 4:The directory
tutorial/bAIes/4-simulation/Contains
cmap_20240524.cmap, however idp_nvt.in requiresdry_ff_20240524_correct.cmapError: ERROR on proc 0: cannot open cmap grid potential file dry_ff_20240524_correct.cmap: No such file or directory (src/potential_file_reader.cpp:59)Changing
dry_ff_20240524_correct.cmapto Containscmap_20240524.cmapresolves the error.I also have a few queries regarding the input files:
cmap_20240524.cmapremain constant for all systems?Thanks
Kartik