Hi rube23,
With plumed, more descriptive error messages can be generally found in the log file. Is what you posted the log file?
I just copied the last part of the log file. Not the complete log.
In general the log is telling you that there is an atom with the index 0. That could be because of errors in your plumed file or because of errors in your reference pdb file. Does that PDB file contain the whole box or only the peptide? Try providing only the peptide
I get that now. I created a pdb file using the command gmx_mpi editconf -f topol.tpr -o pentap.pdb and also corrected the dihedral angle mistake. Now it reads as follows (the complete plumed.dat file:
# Activate MOLINFO functionalities MOLINFO STRUCTURE=pentap.pdb # Compute the backbone dihedral angle phi, defined by atoms C-N-CA-C # you should use MOLINFO shortcuts phi: TORSION ATOMS=@phi-3 # Compute the backbone dihedral angle psi, defined by atoms N-CA-C-N # here also you should to use MOLINFO shortcuts psi: TORSION ATOMS=@psi-4 # Activate well-tempered metadynamics in phi metad: METAD ARG=phi,psi # Deposit a Gaussian every 500 time steps, with initial height # equal to 1.2 kJ/mol and bias factor equal to 8 PACE=500 HEIGHT=1.2 BIASFACTOR=8 # Gaussian width (sigma) should be chosen based on the CV fluctuations in unbiased run # try 1/2 or 1/3 of the estimated fluctuations SIGMA=0.35 # Gaussians will be written to file and also stored on grid FILE=HILLS GRID_MIN=-pi GRID_MAX=pi # Print both collective variables on COLVAR file every 10 steps PRINT ARG=phi,psi FILE=COLVAR STRIDE=10
Looking at your plumed file your definitions of the dihedral angles also seems incorrect to me (@phi-# should be incorrect, it is missing the residue number). See: PLUMED: MOLINFO
Hope this helps, Best
This time I getting the following error message:
– Program: gmx mdrun, version 2024.5-plumed_2.11.0_dev Unknown exception: (exception type: N4PLMD6Plumed14ExceptionErrorE) (core/Action.cpp:375) void PLMD::Action::error(const std::string&) const ERROR in input to action METAD with label metad : keyword SIGMA is compulsory for this action For more information and tips for troubleshooting, please check the GROMACS website at https://manual.gromacs.org/current/user-guide/run-time-errors.html
My understanding is there is some issue with SIGMA parameter. However, I have provided the SIGMA parameter in the configuration file.
Thank you making me progress in understanding my mistakes and troubleshooting @PofPaf . I have attached the .log file this time.
md.log (22.2 KB)
Many thanks,
