GROMACS version:2025.1
GROMACS modification: Yes
I am studying meta-dynamics using PLUMED with GROMACS. Following is my plumed.dat file.
# vim:ft=plumed
MOLINFO STRUCTURE=apom.pdb
# Compute the backbone dihedral angle phi, defined by atoms C-N-CA-C
# you might want to use MOLINFO shortcuts
phi: TORSION ATOMS=@phi-#
# Compute the backbone dihedral angle psi, defined by atoms N-CA-C-N
psi: TORSION ATOMS=@psi-#
# 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
PACE=500 HEIGHT=1.2
# the bias factor should be wisely chosen
BIASFACTOR=_5.0 # Chosen out of blue for this learning
# Gaussian width (sigma) should be chosen based on CV fluctuation in unbiased run
SIGMA=0.35, 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 and the value of the bias potential on COLVAR file
PRINT ARG=phi,psi,metad.bias FILE=COLVAR STRIDE=10
I have searched the forum and majority of the posts says it is a bug. I am attaching my .tpr file for your reference. What should I do to overcome this challenge, if I want to run plumed. I have patched plumed as per the installation instruction mentioned in plumed web-site. Any suggestion, help would be very helpful.
md_0_1.dat (685.5 KB)
I have renamed .tpr to .dat for uploading.
Many thanks,