#################################################################################### # # # Standard Keyfile for ABSINTH LJ + OPLS Force Field # # # #################################################################################### # Simulation Settings ############################################################################## FMCSC_PDBANALYZE 0 # Run a fresh simulation of the system FMCSC_SHAPE 2 # Uses a spherical droplet as the bounding box FMCSC_SIZE 150 # The spherical droplet has a radius of 150 Angstroms FMCSC_BOUNDARY 4 # Use "Atom-Based Soft-Wall" boundary condition FMCSC_NRSTEPS 40000000 # Run the simulation for 41000000 steps FMCSC_EQUIL 10000000 # Discard the first 1000000 steps and do not use them in analysis FMCSC_RANDOMIZE 1 # initial structures random # Hamiltonian ###################################################################################### FMCSC_UAMODEL 0 # Logical to toggle building of aliphatic hydrogens FMCSC_SIGRULE 1 # Calculates pairwise sigma using the arithmetic mean FMCSC_EPSRULE 2 # Calculates pairwise epsilon using the geometric mean FMCSC_SC_IPP 1.0 # Scales inverse power potential (Usually repulsive L-J) FMCSC_SC_ATTLJ 1.0 # Scales strength of dispersive L-J interactions FMCSC_SC_WCA 0.0 # Scaling of Weeks-Chandler-Andersen potential (Independent of L-J) FMCSC_MODE_14 1 # 1-4 Interaction Requirement: Separated by three bonds FMCSC_FUDGE_ST_14 1.0 # Scales 1-4 electrostatic potentials FMCSC_FUDGE_EL_14 1.0 # Scales 1-4 steric/dispersive potentials FMCSC_SC_BONDED_B 0.0 # Scaling factor for bonded potentials (MC = Bond lengths fixed) FMCSC_SC_BONDED_A 0.0 # Scaling factor for angular potentials (MUST BE '1.0' FOR PROLINE) FMCSC_SC_BONDED_I 0.0 # Scaling factor for improper dihedral potentials FMCSC_SC_BONDED_T 1.0 # Scaling factor for torsional potentials FMCSC_SC_EXTRA 0.0 # Scaling factor for structural correction potentials (obselete) FMCSC_SC_POLAR 1.0 # Scaling factor for all polar interactions FMCSC_SC_IMPSOLV 1.0 # Scales the strength of the DMFI FMCSC_SAVPROBE 2.5 # * Radius of solvent (calculates thickness of first solvation layer) FMCSC_IMPDIEL 78.2 # * The value of the dielectric coefficient of the implicit solvent FMCSC_FOSTAU 0.25 # Steepness of sigmoidal interpolation for solvation energy FMCSC_FOSMID 0.1 # Midpoint of sigmoidal interpolation for solvation energy # The above terms used in solvation states for the DMFI FMCSC_SCRMODEL 2 # Screening model for electrostatics FMCSC_SCRTAU 0.5 # Steepness of sigmoidal interpolation for coloumbic screening FMCSC_SCRMID 0.9 # Midpoint of sigmoidal interpolation for coloumbic screening FMCSC_INTERMODEL 1 # Exclusion rules for short-range LJ interactions. This setting # excludes interactions that are defined as frozen with respect # to internal coordinates (e.g. aromatics). Relies on MODE_14 to # determine 1-4 interactions. FMCSC_ELECMODEL 2 # Additional exclusion rules for short-range electrostatic interactions (1 is standard MMFF-like; 2 is ABSINTH-like) FMCSC_SC_ZSEC 1.0 # Scaling factor for global secondary structure bias FMCSC_ZS_FR_B 0.0 # Note that the target beta position is the REX exchange parameter and will be reset FMCSC_ZS_FR_KB 150 # Force constant for beta in kcal/mol FMCSC_ZS_POS_B -152.0 142.0 # Phi/psi angles of the center of the beta region (circle) in degrees FMCSC_ZS_RAD_B 50.0 # Radius of the assumed beta region (circle) in degrees FMCSC_SC_DSSP 0.0 # Scaling factor for DSSP aligning potential (using H/E-Scores) FMCSC_SC_TOR 0.0 # Scaling factor controlling external scaling of torsional bias terms FMCSC_SC_DREST 0.0 # Scaling factor for externally defined harmonic distance restraints FMCSC_SC_TABUL 0.0 # Scaling factor for externally defined tabulated potentials FMCSC_SC_POLY 0.0 # Scaling factor for restraint potentials on polymeric properties (t/δ) FMCSC_SC_EMICRO 0.0 # Scaling factor for restraint potentials on spatial densities FMCSC_GHOST 0 # Scaling factor for "ghosting" interactions of selected particles # Monte Carlo Sampler ############################################################################## FMCSC_RIGIDFREQ 0.01 # Frequency of 3-D rigid moves of the molecule - avoid asymmetric boundary artifacts FMCSC_RIGIDRDFREQ 1.0 FMCSC_CHIFREQ 0.3 # Frequency of side chain torsional moves FMCSC_NRCHI 2 FMCSC_CHIRDFREQ 0.6 FMCSC_CHISTEPSZ 30.0 FMCSC_CRFREQ 0.0 # Frequency of concerted rotation moves FMCSC_OMEGAFREQ 0.1 # Frequency of omega bond moves FMCSC_OMEGARDFREQ 0.1 # Frequency of randomizing omega bond moves amongst all omega moves FMCSC_OMEGASTEPSZ 5.0 # Maximum allowable perturbation in phi/psi torsional angle in stepwise move FMCSC_PIVOTRDFREQ 0.3 # Frequency of randomizing phi/psi moves amongst all phi/psi moves FMCSC_PIVOTSTEPSZ 10.0 # Maximum allowable perturbation in phi/psi torsional angle in stepwise move FMCSC_CLURBFREQ 0.0 # Frequency of moving multiple molecules translationally along a vector FMCSC_PKRFREQ 0.0 FMCSC_PIVOTMODE 1 # Samples all backbone "pivot" moves with equal likelihood FMCSC_COUPLE 0 # Phi and psi moves proposed independently of sidechain moves FMCSC_ALIGN 4 # The molecule swivels around both the C and N termini # Verbose Reports ################################################################################## FMCSC_SEQREPORT 0 # 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 0 # 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 FMCSC_CHECKFREQ 100000 FMCSC_FLUSHTIME 2.0 # OpenMP Settings ################################################################################## FMCSC_NRTHREADS 8 # Number of threads FMCSC_THREADS_DLB_EXT 1 # Data accumulation interval (in steps) for dynamic load balancing (DLB) FMCSC_THREADS_DLB_FREQ 500 # Interval for restarting DLB scheme FMCSC_THREADS_DLB_STOP 250 # Length of each DLB segment # Output Files ##################################################################################### FMCSC_BASENAME _ # Basename used before any output files FMCSC_XYZOUT 5000 # Writes out coordinates to trajectory file FMCSC_ENOUT 5000 # Printout for ENERGY FMCSC_TOROUT 1000000000 # Printout for FYC FMCSC_ACCOUT 5000000000 # Printout for ACCEPTANCE FMCSC_RSTOUT 100000 # Frequency for writing restart files FMCSC_POLOUT 5000 # Data collection for POLYMER FMCSC_RHCALC 5000 # Data collection for INTSCAL and KRATKY FMCSC_SCATTERCALC 100000 # Secondary interval for KRATKY.dat FMCSC_PCCALC 5000000000 # Data collection for AMIDES_PC, RBC_PC, GENERAL_PC FMCSC_SAVCALC 5000000000 # Data collection for SAV and SAV_BY_ATOM FMCSC_ANGCALC 500 # Data collection for JCOUPLING, RAMACHANDRAN FMCSC_SEGCALC 50 # Data collection for BB_SEGMENTS* and ZSEC* FMCSC_POLCALC 500 # Data collection for POLYAVG, RGHIST, RETEHIST, RDHIST FMCSC_DSSPCALC 500 # Data collection for DSSP (H-Bond 2nd Structure) Calc FMCSC_CONTACTCALC 500 # Data collection for CONTACTMAP and CONTACT_HISTS FMCSC_CLUSTERCALC 100000 # Secondary interval for solution structure analysis at molecule level FMCSC_DIPCALC 1000000000 # Data collection for MOLDIPOLES.dat and RESDIPOLES.dat FMCSC_EMCALC 1000000000 # Data collection for spatial densities FMCSC_XYZPDB 4 # Outputs trajectory information as an .xtc file # Input Files ###################################################################################### FMCSC_BBSEGFILE /usr/local/campari/data/bbseg2.dat PARAMETERS /usr/local/campari/params/abs3.2_opls.prm FMCSC_SEQFILE q30.in # Multi-Simulation Varied Parameters ############################################################## FMCSC_TEMP 298.0 # Run the simulation at 298 K # MPI / Replica Exchange settings ################################################################# FMCSC_MPIAVG 0 FMCSC_REMC 1 # Enables replica exchange FMCSC_REFILE remc.in # Replica exchange input file FMCSC_REPLICAS 11 # Number of replicas (must match what was granted by MPI) FMCSC_REDIM 1 # Number of exchange parameters FMCSC_RENBMODE 2 # Only swap with neighboring conditions FMCSC_RESWAPS 10 # Number of swaps per RE cycle FMCSC_REFREQ 10000 # Interval for RE cycles # Cutoff settings ################################################################################## FMCSC_CUTOFFMODE 4 FMCSC_NBCUTOFF 12.0 FMCSC_ELCUTOFF 14.0 FMCSC_N2LOOP 0