Bias exchange metadynamics simulation of the cis-trans isomerization of a Prolyl Peptide
PLUMED input for a bias-exchange metadynamics simulation of the cis-trans isomerization in a Prolyl peptide (see also that of a bi-dimensional metadynamics). The simulation utilizes two replicas, each applying a bias to one of the torsion angles, omega and psi, that describe the cis-trans transition at the proline peptide bond, along with the associated auxiliary conformational motion, respectively. Replica exchanges are attempted at regular intervals and accepted according to a Metropolis criterion, based on the biasing potentials of the replicas.
The setup entails one common PLUMED file specifing the two torsional angles, omega and psi, and the RANDOM_EXCHANGES keyword instructing PLUMED to make exchanges between randomly chosen replicas:
# randomize the exchange (not between consecutive indeces, here just 2 replicas, so it is not relevant) RANDOM_EXCHANGESSet random pattern for exchanges. More details # set up the two torsion collective variables # omega (use cv1 so it will be compatible with the METAGUI analysis plugin) cv1: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=19,26,28,3 # psi (use cv2 so it will be compatible with the METAGUI analysis plugin) cv2: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=27,31,39,41
Two additional PLUMED files are required for each metadynamics replica, and these can be placed in separate folders where each replica is being run. These PLUMED files read the definitions of collective variables and other shared parameters from the common PLUMED file using the INCLUDE FILE keyword. The bias is applied to a single dihedral angle, with each replica biasing a different angle. The first PLUMED file performs metadynamics on the omega angle (cv1):
INCLUDEIncludes an external input file, similar to #include in C preprocessor. More details. Show included file FILEfile to be included=plumed_be-common.dat
#METAD activates metadynamics #ARG indicates variables to enhance (omega & psi) #PACE indicates frequency of Gaussian deposition is 1000 time step (2ps) #HEIGHT indicates that height of the Gaussians is 0.2 kJ/mol #SIGMA indicates the width of the Gaussians on the biased cv, respectively
be: METADUsed to performed metadynamics on one or more collective variables. This action has hidden defaults. More details ARGthe labels of the scalars on which the bias will act=cv1 PACEthe frequency for hill addition=1000 HEIGHTthe heights of the Gaussian hills=0.2 SIGMAthe widths of the Gaussian hills=0.17
#print in other file the values of the CVS and the bias potential #STRIDE frequency of output #ARG things to print, omega, psi #FILE, name of the file to output; COLVAR
PRINTPrint quantities to a file. More details STRIDE the frequency with which the quantities of interest should be output=500 ARGthe labels of the values that you would like to print to the file=cv1,cv2 FILEthe name of the file on which to output these quantities=COLVAR DUMPFORCESDump the force acting on one of a values in a file. More details ARGthe labels of the values whose forces should be output=cv1,cv2 STRIDE the frequency with which the forces should be output=500 FILEthe name of the file on which to output the forces=forces.dat
The second PLUMED file entails a metadynamics on the psi angle (cv2):
INCLUDEIncludes an external input file, similar to #include in C preprocessor. More details. Show included file FILEfile to be included=plumed_be-common.dat
#METAD activates metadynamics #ARG indicates variables to enhance (omega & psi) #PACE indicates frequency of Gaussian deposition is 1000 time step (2ps) #HEIGHT indicates that height of the Gaussians is 0.2 kJ/mol #SIGMA indicates the width of the Gaussians on the biased cv, respectively
be: METADUsed to performed metadynamics on one or more collective variables. This action has hidden defaults. More details ARGthe labels of the scalars on which the bias will act=cv2 PACEthe frequency for hill addition=1000 HEIGHTthe heights of the Gaussian hills=0.2 SIGMAthe widths of the Gaussian hills=0.24
#print in other file the values of the CVS and the bias potential #STRIDE frequency of output #ARG things to print, omega, psi #FILE, name of the file to output; COLVAR
PRINTPrint quantities to a file. More details STRIDE the frequency with which the quantities of interest should be output=500 ARGthe labels of the values that you would like to print to the file=cv1,cv2 FILEthe name of the file on which to output these quantities=COLVAR DUMPFORCESDump the force acting on one of a values in a file. More details ARGthe labels of the values whose forces should be output=cv1,cv2 STRIDE the frequency with which the forces should be output=500 FILEthe name of the file on which to output the forces=forces.dat
Both PLUMED files output the collective variables and biasing applied forces on those variables to the files COLVAR and forces.dat via the keywords PRINT and DUMPFORCES, respectively. These files are useful for calculating the bi-dimensional free energy as a function of omega and psi, using the sampling of both replicas via the force correction analysis method (FCAM, Marinelli et al. JCTC 2021, https://github.com/FCAM-NIH/FCAM). Detailed documentation on setup and analysis is provided on the Tutorial Instructions.