#################################################################################### # # # Keyfile for Tutorial 4 - Testing Movesets # # # #################################################################################### # Simulation Settings ############################################################################## FMCSC_PDBANALYZE 0 # Run a fresh simulation of the system FMCSC_SHAPE 1 # Shape of bounding box FMCSC_SIZE 40.0 40.0 40.40 # Dimensions of bounding box FMCSC_BOUNDARY 1 # Boundary conditions FMCSC_NRSTEPS 20000000 # Total steps FMCSC_EQUIL 0 # Number of steps discarded as equilibration period FMCSC_RANDOMIZE 1 # Use random initial starting structure FMCSC_TEMP 312.0 # Simulation Temperature # Hamiltonian ###################################################################################### PARAMETERS /params/abs3.2_charmm36.prm FMCSC_SC_IPP 0.0 # Scales inverse power potential (Usually repulsive L-J) FMCSC_SC_BONDED_B 1.0 # Scaling factor for bonded potentials FMCSC_SC_BONDED_A 1.0 # Scaling factor for angular potentials # Monte Carlo Sampler ############################################################################## FMCSC_MC_ACCEPT 1 # Criterion used to accept/reject Monte Carlo moves (1 is Metropolis) FMCSC_ALIGN 4 # What is the base of motion for backbone pivot moves (4 is stochastic but tends to move the shorter segment) FMCSC_RIGIDFREQ 0.2 # Frequency of 3-D rigid-body moves of molecules FMCSC_TRANSSTEPSZ 10.0 # Max step size for rigid-body translation FMCSC_ROTSTEPSZ 30.0 # Max step size for rigid-body rotation FMCSC_COUPLERIGID 1 # Logical determining if single-molecule rigid-body moves move translational and rotational d.o.f.s jointly FMCSC_CLURBFREQ 0.2 # Frequency of moving multiple molecules in concerted fashion FMCSC_CLURBMAX 3 # Maximum number of "cluster" size for concerted moves FMCSC_CLURBROTFREQ 0.6 # Multi-molecule rigid-body moves have three variants: this is the branch frequency for pivoting and spinning (the rest is translation) FMCSC_CLURBSPINFREQ 0.5 # Frequency of spinning moves within spinning/pivoting branch FMCSC_RIGIDRDFREQ 0.5 # Fraction of fully randomizing rigid body moves for all rigid-body move classes FMCSC_CHIFREQ 0.1 # Frequency of side chain torsional (chi) moves FMCSC_CHIRDFREQ 0.5 # Fraction of fully randomizing chi moves FMCSC_NRCHI 4 # Maximum number of concurrently sampled chi-angles FMCSC_CHISTEPSZ 20.0 # Max step size for stepwise chi moves FMCSC_OMEGAFREQ 0.1 # Frequency of omega bond moves FMCSC_OMEGARDFREQ 0.5 # Fraction of fully randomizing omega moves FMCSC_OMEGASTEPSZ 10.0 # Max step size for stepwise omega moves FMCSC_PIVOTRDFREQ 0.5 # Fraction of fully randomizing phi/psi moves FMCSC_PIVOTSTEPSZ 10.0 # Max step size for stepwise phi/psi moves FMCSC_PKRFREQ 0.1 # Frequency of proline pucker moves FMCSC_PKRRDFREQ 0.1 # Frequency of reflection moves in proline pucker FMCSC_PUCKERSTEP_DI 4.0 # Max step size for torsions in stepwise pucker moves (also for sugar) FMCSC_PUCKERSTEP_AN 2.0 # Max step size for angles in stepwise pucker moves (also for sugar) FMCSC_CRFREQ 0.2 # Frequency of moving a concerted section of the backbone FMCSC_CRMODE 1 # Method for building differential matrix for Sjunnesson concerted rotation FMCSC_CRWIDTH 0.1 # Standard deviation of displacement vectors used in Sjunnesson CR FMCSC_CRDOF 8 # Number of torsions to use in each Sjunnesson CR move FMCSC_CRBIAS 10.0 # Controls how far the end of the rotated segment lands to its original position in SJ CR FMCSC_ANGCRFREQ 0.0 # Fraction of CR moves that use the Ulmschneider-Jorgensen (UJ) method FMCSC_TORCRFREQ 0.8 # Fraction of exact torsional concerted rotation moves on remaining CR Moves FMCSC_TORCROFREQ 0.5 # Fraction of those that include omega bond in prerotation segment FMCSC_UJCRBIAS 10.0 # Regulates the bias of the pre-rotation segment toward possible closures in exact CR methods FMCSC_UJCRWIDTH 5.0 # Regulates width of the distribution sampled in pre-rotation in exact CR method FMCSC_UJCRSTEPSZ 1.0 # (Maximum) stepsize for the root-search in exact CR methods FMCSC_TORCRMODE 1 # Whether to use maxtries when trying torsional CR (here: no) FMCSC_TORCRMIN_DO 1 # Minimum number of pre-rotation degrees of freedom for torsional CR with omega FMCSC_TORCRMAX_DO 3 # Maximum number of pre-rotation degrees of freedom for torsional CR with omega FMCSC_TORCRMIN_DJ 1 # Minimum number of pre-rotation degrees of freedom for torsional CR FMCSC_TORCRMAX_DJ 3 # Maximum number of pre-rotation degrees of freedom for torsional CR FMCSC_TORCRSCOME 0.5 # Scale down the relative magnitude of omega step-size in pre-rotation for CR with omega FMCSC_NUCFREQ 0.4 # Frequency of sampling nucleotide backbone degrees of freedom FMCSC_NRNUC 4 # Maximum number of nucleotide backbone dihedral angles to sample in a single pivot move FMCSC_NUCRDFREQ 0.5 # Fraction of randomizing pivot moves for nucleotides FMCSC_NUCSTEPSZ 20.0 # Max step size for stepwise pivot moves of nucleotides FMCSC_SUGARFREQ 0.3 # Frequency of sugar pucker moves in nucleotides FMCSC_SUGARRDFREQ 0.1 # Frequency of reflection moves in sugar rings FMCSC_NUCCRFREQ 0.3 # Frequency of exact torsional CR moves for nucleic acids FMCSC_NUCCRMIN 1 # Minimum number of pre-rotation degrees of freedom in nucleotide CR FMCSC_NUCCRMAX 3 # Maximum number of pre-rotation degrees of freedom in nucleotide CR FMCSC_OTHERFREQ 0.2 # Frequency for single torsion pivot moves FMCSC_OTHERUNKFREQ 0.0 # Fraction of those operating on degrees of freedom in unsupported residues FMCSC_OTHERNATFREQ 0.25 # Fraction of those operating on native CAMPARI degrees of freedom FMCSC_OTHERRDFREQ 0.5 # Fraction of randomizing single torsion pivot moves FMCSC_OTHERSTEPSZ 20.0 # Max step size for stepwise single torsion pivot moves # Reporting and Run Diagnosis ###################################################################### FMCSC_FLUSHTIME 1.0 # Interval for flushing (committing I/O buffer of) running output files in minutes (also prints remaining run time estimate) FMCSC_SEQREPORT 1 # Prints out a summary of sequence features FMCSC_DIPREPORT 0 # Prints out a summary of determined charge groups FMCSC_VDWREPORT 0 # Prints out a summary of van der Waals parameters FMCSC_FOSREPORT 0 # Prints out a summary of free energies of solvation FMCSC_BONDREPORT 1 # Prints out a summary of bonded potentials FMCSC_ELECREPORT 0 # Prints out a summary of close-range electrostatics FMCSC_INTERREPORT 0 # Prints out a summary of short-range interactions # Output Files ##################################################################################### FMCSC_BASENAME movesets # Basename used before any output files FMCSC_XYZOUT 10000000000000 # Data printout for trajectory file FMCSC_ENOUT 10000 # Data printout for ENERGY FMCSC_PHOUT 100000000000000 # Data printout for pH in MC FMCSC_TOROUT -100 # Data printout for FYC (negative value means to print only sampled (rather than only native) d.o.f.s) FMCSC_ACCOUT 100 # Data printout for ACCEPTANCE FMCSC_RSTOUT 10000000000000 # Data printout for restart files FMCSC_POLOUT 10000000000000 # Data printout for POLYMER FMCSC_RHCALC 10000000000000 # Data collection for INTSCAL and KRATKY FMCSC_PCCALC 20 # Data collection for AMIDES_PC, RBC_PC, GENERAL_PC FMCSC_SAVCALC 1000000000000 # Data collection for SAV and SAV_BY_ATOM FMCSC_COVCALC 2000000000000 # Data collection for degrees of freedom FMCSC_ANGCALC 20 # Data collection for JCOUPLING, RAMACHANDRAN FMCSC_RAMARES 2 6 13 # Specific Ramachandran analysis per residue FMCSC_ANGRES 6.0 # Resolution for accumulated ANGCALC data FMCSC_INTCALC 10 # Data collection for internal coordinate histograms FMCSC_WHICHINT 1 1 1 1 # Request histograms for all four types of internals FMCSC_SEGCALC 1000000000000 # Data collection for BB_SEGMENTS and Z HISTS FMCSC_DIPCALC 1000000000000 # Data collection for MOLDIPOLES and RESDIPOLES FMCSC_POLCALC 2000000000000 # Data collection for POLYAVG, RGHIST, RETEHIST, RDHIST FMCSC_DSSPCALC 100000000000 # Data collection for DSSP (H-Bond 2nd Structure) Calc FMCSC_HOLESCALC 10000000000 # Data collection for HOLES ("Void spaces") FMCSC_DIFFRCALC 10000000000 # Data collection for DIFFRACTION ("Fiber diffraction") FMCSC_CONTACTCALC 2000000000 # Data collection for CONTACTMAP and CONTACT_HISTS # Input Files ###################################################################################### FMCSC_SEQFILE tutorial4.seq FMCSC_ANGRPFILE tutorial4.agp # MPI settings FMCSC_MPIAVG 1 # This type of calculation is perfect for MPI data pooling FMCSC_REMC 0 # Disable explicitly (since these two options conflict) # Varying Paramters ################################################################################