| bomlev | undef | set bomb level |
| prnlev | undef | set print level |
| ioformat | undef | set ioformat: 'exte' or 'noex' |
| |
| param | 36 | parameter set: 19 (CHARMM19), 22 (CHARMM22), opls, a94 (amber 94), eef1, mmff, eef1.1 |
| |
| xtop | undef | extra topology files |
| xpar | undef | extra parameter files |
| pstream | undef | extra topology/parameter files to be streamed |
| parflex | undef | add 'flex' when reading parameters/topologies |
| |
| blocked | undef | blocked termini |
| nter | undef | N-terminus, requires blocked |
| cter | undef | C-terminus, requires blocked |
| nuc3ter | undef | nucleic acid 3" terminus |
| nuc5ter | undef | nucleic acid 5" terminus |
| deoxy | 1 | deoxy patch for nucleic acids |
| terlist | undef | explicit list of termini, format: SEG:FIRST:LAST[=...] |
| fixcoo | 1 | fix COO if necessary |
| |
| hsd | "" | list of HSD residues |
| hse | "" | list of HSE residues |
| hsp | "" | list of HSP residues |
| |
| resmod | "" | list of residue name modifications |
| |
| patch | "" | list of patches |
| autogen | 1 | auto generate angles/dihedrals after patches |
| solvseg | undef | segments to be loaded with water after everything else |
| |
| buildall | 1 | rebuild all missing atoms |
| hbuild | 0 | force hbuild |
| |
| faster | "on" | fast energy routines (on|off) |
| |
| dielec | 'CDIE' | dielectric response CDIE (const.) or RDIE (distant dep.) |
| epsilon | 1.0 | dielectric constant for non-bonded interactions |
| cutnb | undef | cutoff for non-bonded list generation |
| cutoff | undef | cutoff for non-bonded interactions |
| cuton | undef | onset of switching function for non-bonded interaction |
| cutim | undef | cutoff for image atoms |
| cut | 1 | use cutoff |
| crystalcut | undef | cutoff for crystal |
| trunc | undef | shift/fshift/switch/fswitch |
| vtrunc | undef | vshift/vfshift/vswitch/vfswitch |
| nbmode | "atom" | atom or group |
| vdwlrc | 0 | van der Waals long range correction |
| softvdw | 0 | soft van der Waals core |
| softemax | undef | maximum van der Waals energy |
| softmine | undef | minimum attractive energy |
| softmaxe | undef | maximum electrostatic energy |
| |
| user | 1 | USER energy term |
| cmap | 1 | CMAP energy term |
| |
| echeck | 20.0 | energy tolerance check for dynamics |
| |
| ace | 0 | ACE implicit solvation |
| aceieps | 1.0 | ACE internal dielectric |
| aceseps | 80.0 | ACE external dielectric |
| acealpha | 1.3 | ACE alpha |
| acesigma | undef | ACE sigma |
| acevscale | 1.0 | ACE volume scale |
| |
| sasagamma | 0.00542 | gamma for SASA |
| sasadelta | 0.920 | delta for SASA |
| |
| gb | undef | Generalized Born implicit solvent: bgb, gbmf, gbmf2, gbmva, gbmvg |
| gbeps | 80.0 | epsilon in GB prefactor |
| |
| gbcrad | 0.91 | BGB radius scaling of main chain carbon w/ param19 |
| gbhrad | 0.8 | BGB radius scaling of hydrogen atoms w/ param22 |
| gblambda | undef | BGB lambda factor |
| |
| gbmvad | undef | GBMVA shift |
| gbmvade | undef | GBMVA eshift |
| gbmvas | undef | GBMVA slope |
| gbmval1 | 0.5 | GBMVA lambda 1 |
| gbmvap1 | 0.45 | GBMVA P1 |
| gbmvap2 | 1.25 | GBMVA P2 |
| gbmvap3 | 0.65 | GBMVA P3 (old: 0.70) |
| gbmvap4 | undef | GBMVA P4 |
| gbmvap5 | undef | GBMVA P5 |
| gbmvap6 | 8.0 | GBMVA P6, Still's factor |
| gbmvap7 | undef | GBMVA P7, VSA adjustment |
| gbmvaig | 32 | GBMVA integration grid size |
| gbmvafrq | undef | GBMVA alpha update frequency |
| gbmvdrfrq | undef | GBMVA surface integration point update frequency |
| gbmvaimp | undef | GBMVA impulse derivatives |
| gbmvaemp | undef | GBMVA exponentially damped impulse |
| gbmvarith | undef | GBMVA arithmetic mean: alpha_ij = alpha_i+alpha_j |
| gbmvabuf | 0.2 | GBMVA buffer for dynamics |
| gbmvabeta | -12 | GBMVA beta parameter (old: -20) |
| gbmvaonx | 1.9 | GBMVA OnX parameter |
| gbmvaoffx | 2.1 | GBMVA OffX parameter |
| gbmvacubic | undef | GBMVA cubic VSA |
| gbmvacorr | 1 | GBMVA r7 correction (1) or r5 correction (0) |
| gbmvaextra | undef | GBMVA extra commands |
| gbmvagcut | undef | GBMVA GCUT (1 or 2) |
| gbmvakappa | undef | GBMVA kappa |
| gbmvafast | undef | GBMVA FAST |
| gbmvasgbfrq | 4 | GBMVA SGBFRQ |
| gbmvasxd | 0.3 | GBMVA SGBFRQ delta |
| |
| gbmva1 | undef | GBMV A1 parameter |
| gbmva2 | undef | GBMV A2 parameter |
| gbmva3 | undef | GBMV A3 parameter |
| gbmva4 | undef | GBMV A4 parameter |
| gbmva5 | undef | GBMV A5 parameter |
| gbmvdf | undef | GBMV adjustment factor for shift |
| gbmvdoff | undef | GBMV epsilon offset for shift adjustment |
| gbmvmstl | undef | GBMV modified Still |
| gbmvms0 | 1.0 | GBMV MS0 parameter |
| gbmvms1 | 0.0 | GBMV MS1 parameter |
| gbmvms2 | 0.0 | GBMV MS2 parameter |
| gbmvms3 | 0.0 | GBMV MS3 parameter |
| |
| gbmvdefmnp | 0 | turn on default membrane non-polar profile |
| gbmvzs | 0.5 | parameters for membrane non-polar profile |
| gbmvzm | 9.2 | parameters for membrane non-polar profile |
| gbmvzt | 25 | parameters for membrane non-polar profile |
| gbmvst | 0.32 | parameters for membrane non-polar profile |
| |
| gbmveps | undef | GBMV solvent dielectric |
| gbmvepsu | undef | GBMV solute ref dielectric |
| |
| gbmvdu | undef | GBMV adj. delta for solute dielectric |
| |
| gbmvsa | 0.015 | GBMV hydrophobic SASA term factor |
| gbmvsb | 0.900 | GBMV hydrophobic SASA term offset |
| gbmvsagb | undef | GBMV hydrophobic SASA term on a selection basis |
| |
| gbmvason | 1.2 | GBMV SASA internal parameter, old: 0.5 |
| gbmvasoff | 1.5 | GBMV SASA internal parameter, old: 1.75 |
| |
| #gbmvexcl | 0 | GBMV selection |
| |
| gbswsw | 0.3 | GBSW switching length |
| gbswrmax | 20.0 | GBSW maximum integration radius |
| gbswnang | 38 | GBSW number of angular integration points |
| gbswnrad | 0 | GBSW number of radial integration points |
| gbswsgamma | 0.00 | GBSW surface tension coefficient |
| gbswdgp | 1.5 | GBSW grid spacing for lookup table |
| gbswrbuffer | 0.0 | GBSW buffer region for lookup table |
| gbswtmemb | 0.0 | GBSW thickness of membrane |
| gbswmsw | 0.3 | GBSW membrane switching length |
| gbswms | 0 | GBSW molecular surface approx. |
| |
| hdgbprofile | undef | epsilon profile for HDGB |
| hdgbnpprofile | undef | non-polar profile for HDGB |
| hdgbdensh2oprofile | undef | density profile for water (HDGB van der Waals) |
| hdgbdensoprofile | undef | density profile for O (HDGB van der Waals) |
| hdgbdenscprofile | undef | density profile for C (HDGB van der Waals) |
| hdgbdensccprofile | undef | density profile for CC (HDGB van der Waals) |
| hdgbdenshprofile | undef | density profile for H (HDGB van der Waals) |
| |
| hdgbvdw | 0 | turn on HDGB van der Waals term |
| hdgbvdwact3 | 0.25 | HDGB van der Waals a for CT3 |
| hdgbvdwacy | 0.2 | HDGB van der Waals a for CY |
| hdgbvdwacph | 0.4 | HDGB van der Waals a for CPH |
| hdgbvdwacc | 0.4 | HDGB van der Waals a for CC |
| hdgbvdwaca | 0.2 | HDGB van der Waals a for CA |
| hdgbvdwact1 | 0.55 | HDGB van der Waals a for CT1 |
| hdgbvdwact2 | 0.45 | HDGB van der Waals a for CT2 |
| hdgbvdwacm | 0.7 | HDGB van der Waals a for CM |
| hdgbvdwahs | 0.5 | HDGB van der Waals a for HS |
| hdgbvdwaho | 0.75 | HDGB van der Waals a for HO |
| hdgbvdwahy | 0.2 | HDGB van der Waals a for HY |
| hdgbvdwahm | 0.675 | HDGB van der Waals a for HM |
| hdgbvdwahp | 0.15 | HDGB van der Waals a for HP |
| hdgbvdwahr | 0.475 | HDGB van der Waals a for HR |
| hdgbvdwanh | 0.225 | HDGB van der Waals a for NH |
| hdgbvdwany | 0.15 | HDGB van der Waals a for NY |
| hdgbvdwaoh | 0.75 | HDGB van der Waals a for OH |
| hdgbvdwaoy | 0.725 | HDGB van der Waals a for OY |
| hdgbvdwaor | 0.425 | HDGB van der Waals a for OR |
| hdgbvdwasm | 0.175 | HDGB van der Waals a for SM |
| hdgbvdwasc | 0.425 | HDGB van der Waals a for SC |
| hdgbvdwas | 0.225 | HDGB van der Waals a for S |
| hdgbvdwap | 0.375 | HDGB van der Waals a for P |
| |
| scalerad | 0 | scaled radii for GB/PB |
| |
| dcel | 0.5 | PB grid spacing |
| epsw | 80.0 | epsilon for solvent |
| epsp | 1.0 | epsilon for solute |
| epspr | undef | epsilon for solute reference if set |
| epsr | 1.0 | epsilon for reference environment |
| smooth | 0 | smooth boundary |
| pbdelta | 8.0 | distance to boundary |
| proberad | 1.4 | water probe radius |
| pbionr | 2.0 | ion exclusion radius |
| pbionconc | 0.0 | ion concentration |
| pbtemp | 300.0 | temperature |
| pbextra | "" | extra parameters for PBEQ |
| pbepsfile | undef | external file for dielectric grid (first type) |
| pbepsgrid | undef | external file for dielectric grid (second type) |
| |
| chargefile | undef | load charges from external file |
| |
| volumespace | 200000 | space for volume calculation |
| rdfrmax | undef | maximum radius for RDF analysis |
| rdfbins | 100 | number of bins for RDF analysis |
| rdfspfac | 10 | space allocation for RDF analysis |
| rdfvolume | undef | normalization volume for RDF analysis |
| rdfexclude | undef | bygr, byres, byseg to exclude self pairs |
| diffrange | undef | distance range for diffusion calculation |
| ncors | 20 | number of time steps for diffusion/correlation calculation |
| puckermode | "AS" | AS or CP pucker calculation |
| ptype | "P1" | P1 or P2 correlation |
| |
| sradfac | 1.0 | overall scaling factor for GB/PB radii |
| sbackn | 1.0 | 0.90, # peptide backbone N scaling factor |
| sbacko | 1.0 | 0.94, # peptide backbone O scaling factor |
| sbackca | 1.0 | peptide backbone CA scaling factor |
| |
| mfnh | undef | radius for H* |
| mfn3 | undef | radius for ch3 |
| mfn2 | undef | radius for cb |
| mfnb10 | undef | radius for backbone CA (GLY) |
| mfnb9 | undef | radius for backbone CA |
| mfnb6 | undef | radius for backbone C |
| mfnb7 | undef | radius for backbone O |
| mfnb8 | undef | radius for backbone N |
| mfn5 | undef | radius for ch |
| mfn13 | undef | radius for roh |
| mfn12 | undef | radius for oh |
| mfn4 | undef | radius for cet |
| mfn19 | undef | radius for crh |
| mfn18 | undef | radius for cpro |
| mfn7 | undef | radius for ctrp |
| mfn16 | undef | radius for ntrp |
| mfn8 | undef | radius for css |
| mfn17 | undef | radius for sulfur |
| mfn25 | undef | radius for s2 |
| mfn6 | undef | radius for cam |
| mfn15 | undef | radius for nam |
| mfn11 | undef | radius for oam |
| mfn10 | undef | radius for ocar |
| mfn9 | undef | radius for cze |
| mfn14 | undef | radius for nal |
| mfn21 | undef | radius for nhis |
| |
| nina9 | undef | radius for ARG CZ |
| nina9l | undef | radius for LYS CE |
| nina10 | undef | radius for GLU/ASP OE*/OD* |
| nina11 | undef | radius for ASN/GLN OE*/OD* |
| nina14 | undef | radius for ARG NH*/NE |
| nina14l | undef | radisu for LYS NZ |
| nina7 | undef | radius for TRP CE*/CD*/CZ*/CH2 |
| nina16 | undef | radius for TRP NE1 |
| nina12 | undef | radius for OG* |
| nina3 | undef | radius for CG* |
| ninah | undef | radius for H* |
| ninab1 | undef | radius for backbone CAY/CAT |
| ninab2 | undef | radius for backbone CY |
| ninab3 | undef | radius for backbone OY |
| ninab4 | undef | radius for backbone NT |
| ninab5 | undef | radius for backbone OT* |
| ninab6 | undef | radius for backbone C |
| ninab7 | undef | radius for backbone O |
| ninab8 | undef | radius for backbone N |
| ninab9 | undef | radius for backbone CA |
| ninab10 | undef | radius for backbone CA (GLY) |
| nina2 | undef | radius for CB |
| nina4 | undef | radius for GLU CG |
| nina5 | undef | radius for CD* |
| nina6 | undef | radius for GLN CD/ASN CG/GLU CD/ASP CG |
| nina18 | undef | radius for PRO GB/CG/CD |
| nina19 | undef | radius for TYR/PHE CE*/CD*/CZ |
| nina8 | undef | radius for MET CE |
| nina20 | undef | radius for HSD CE1/HSD CD2 |
| nina13 | undef | radius for TYR OH |
| nina21 | undef | radius for HSD NE2/ND1 |
| nina22 | undef | radius for HSP NE2/ND1 |
| nina15 | undef | radius for GLN NE2/ASN ND2 |
| nina17 | undef | radius for S* |
| |
| asp | 0 | flag to switch on ASP energy terms |
| aspfile | undef | external input file for ASP energy term |
| aspval | 5.42 | ASP solvation parameter |
| aspvalc | undef | ASP solvation parameter for carbon atoms |
| aspvaln | undef | ASP solvation parameter for nitrogen atoms |
| aspvalo | undef | ASP solvation parameter for oxygen atoms |
| aspvalh | undef | ASP solvation parameter for hydrogen atoms |
| aspvals | undef | ASP solvation parameter for sulphur atoms |
| aspradh | undef | ASP hydrogen radius |
| aspref | 0.0 | ASP reference area |
| |
| og | 0 | flag to switch on Olgun's energy score |
| |
| eef1 | 0 | flag to switch on EEF1 energy terms |
| eef1file | "solvpar.inp" | EEF1 parameter file |
| |
| imm1 | 0 | implicit membrane model based on EEF1, use eef1file for loading parameter file |
| imm1p36 | 0 | imm1 model with using CHARMM36 all-atom parameters |
| imm1file | "solvpar.inp" | IMM1 parameter file |
| imm1width | 26.0 | membrane width |
| imm1aemp | 0.85 | parameter a |
| |
| sasa | 0 | flag to switch on SASA energy terms |
| sasaeps | 2.0 | SASA dielectric constant |
| sasasig1 | -0.060 | SASA sig 1 value |
| sasasig2 | 0.012 | SASA sig 2 value |
| sasasig3 | 0.00 | SASA sig 3 value |
| |
| sdsteps | 50 | number of minimization steps for steepest descent min. |
| sdstepsz | 0.005 | initial step size for steepest descent min. |
| updnbsd | -1 | update freq. for non-bonded list in steepest descent min. |
| |
| minmode | "abnr" | minimization protocol |
| minsteps | 500 | number of minimization steps for min. |
| minstepsz | 0.005 | initial step size for min. |
| minetol | 1.0E-5 | energy tolerance for min. |
| minupdnb | -1 | update freq. for non-bonded list in min. |
| minoutfrq | 10 | output freq. for minimization runs |
| |
| shake | 0 | use shake |
| shaketol | 1.0E-8 | shake tolerance |
| shakemode | 'hyd' | 'hyd'rogen or 'all' atoms are restrained |
| shakefast | 0 | use fast vector/parallel version of shake |
| |
| periodic | undef | use periodic boundaries |
| explicit | 1 | do not use implicit solvent for explicit solvent |
| solvent | undef | residue names of solvent molecules for PBC |
| imbyseg | undef | residue images by segment |
| imbyres | undef | residue images by residue |
| imbysegx | 0.0 | center for images by segment |
| imbysegy | 0.0 | center for images by segment |
| imbysegz | 0.0 | center for images by segment |
| imbyresx | 0.0 | center for images by segment |
| imbyresy | 0.0 | center for images by segment |
| imbyresz | 0.0 | center for images by segment |
| ewald | 1 | use Ewald for explicit solvent |
| pmekappa | undef | 0.32, # PME distribution width |
| pmekmax | 5.0 | 5.0, # PME K max |
| npme | undef | 64, # number of grid points for PME grid |
| npmex | undef | number of grid points in x direction |
| npmey | undef | number of grid points in y direction |
| npmez | undef | number of grid points in z direction |
| |
| boxshape | undef | box shape for periodic boundaries |
| boxsize | undef | box size |
| boxx | undef | box x dimension |
| boxy | undef | box y dimension |
| boxz | undef | box z dimension |
| |
| dynens | 'NVT' | dynamics ensemble 'NVT', 'NPT', 'NPH', 'NVE' |
| dynber | 0 | use Berendsen thermostat |
| dynbertc | 5.0 | coupling constant for Berendsen |
| dynnose | undef | use Nose-Hoover thermostat |
| dynnoseq | 50.0 | Nose-Hoover qref |
| dynnosen | 5 | Nose-Hoover ncyc |
| dyninteg | undef | ovverride default integrator choices: leap, vver, vv2 |
| dyntstep | 0.002 | dynamics time step in picoseconds |
| dynsteps | 100 | dynamics steps |
| dyntemp | 298 | dynamics temperature |
| dynitemp | undef | initial temperature for heating/equilibration |
| dynseed | undef | dynamics random seed |
| dyndeltat | 10.0 | temperature change during heating/cooling |
| dynhtfrq | -1 | temperature change frequency |
| dyntrfrq | undef | trans/rot removal frequency |
| dyneqfrq | 200 | equilibration frequency |
| dyntwin | 5.0 | temperature window during equilibrition |
| dynscale | undef | temperature scaling factor for restarts |
| dynoutfrq | undef | frequency of energy/trajectory output |
| dynupdnb | -1 | update of non-bonded list |
| dynupdimg | -1 | update of images |
| dynpress | 1.00 | the pressure (in atm) for NPT simulations |
| dynpgamma | 25.0 | gamma value for NPT simulations |
| dynpmass | 400.0 | Langevin piston mass for NPT simulations |
| dynpext | 0 | Use external virial in NPT simulations |
| nblisttype | "bycb" | non-bonded list generation |
| dyncons | undef | KDYN dynamics |
| dynkmas | 0.1 | KDYN dynamics mass |
| dynkfkc | undef | KDYN FKC |
| dynkdkc | undef | KDYN DKC |
| |
| phmd | 0 | PHMD |
| phmdpar | undef | PHMD parameter file |
| phmdph | 7.0 | simulation pH |
| phmdpri | 1000 | print output file every 1000 steps |
| phmdmass | 10.0 | mass for the titration and tautomer interconversion coordinates |
| phmdbarr | 2.5 | titration barrier |
| phmdbartau | 2.5 | tautomer interconversion barrier |
| phmdtemp | 298 | PHMD temperature |
| phmdout | "final.lamb" | output file of lambda values |
| phmdderi | undef | compute derivatives |
| phmdtheta | undef | theta value if phmdderi defined |
| phmdthetax | undef | thetax value if phmdderi defined |
| phmdsel | undef | selection of titrating residues |
| |
| sgmd | 0 | self-guided MD |
| sgmddrag | 0.2 | SGMD drag force |
| sgmdavg | 1.0 | SGMD average? |
| sgmdvfb | -1.0 | SGMD ? |
| sgmdfrq | 1 | SGMD update frequency |
| |
| sgld | 0 | self-guided Langevin dynamics |
| sgbz | 0 | option for SGLDfp simulation (Boltzman Dist.) |
| sgldtsvg | 0.2 | local avg time |
| sgldtsvp | 10 | guiding effect avg time |
| sgldtpsg | 1.0 | giding temperature |
| sgldsgft | 0.0 | guiding factor |
| sgldsgmv | 0 | allow guiding force on center of mass |
| sgldistr | 1 | index of the first atom for guiding force application |
| sgldiend | "natom" | index of the last atom for guiding force application |
| |
| noerest | undef | file name with NOE restraint commands |
| xnoerest | undef | X-plor file name with NOE restraint commands |
| noerexp | 3 | exponent for distance averaging |
| noekmin | 1.0 | force constant for small distance harmonic potential |
| noekmax | 1.0 | force constant for large distance harmonic potential |
| noefmax | 9999.0 | maximum force |
| noescale | 1.0 | overall scaling factor |
| noemindist | 0 | use minimum distance for multiple atoms |
| |
| nlambda | 10 | number of windows for PERT sampling |
| pequi | 1000 | number of equilibration steps |
| pprod | 4000 | number of production steps |
| ilambda | undef | run individual lambda step (0 .. nlambda) |
| |
| #qfep | 0 | charging FEP |
| #qfepfix | 1 | fix segment |
| |
| |
| dynextra | undef | extra dynamics command |
| |
| qcor | undef | Ewald charge correction |
| whamtol | 0.001 | WHAM tolerance |
| whamsteps | 200 | WHAM iteration steps |
| whammaxtime | 1000000 | WHAM maximum time |
| whammaxwin | 200 | WHAM maximum number of windows |
| |
| tamd | 0 | Turn on torsion-angle MD, also turns on Berendsen heat bath |
| tamdsetup | undef | Torsion-angle MD tree setup code, standard tree setup if not given |
| |
| dyntp | undef | turn on TP control |
| dyntpcmda | 0 | TPControl dampening of center of mass motion |
| dyntptau | 0.05 | characteristic thermostat response time in ps |
| dyntppress | 1.0 | set reference pressure |
| dyntpbtau | 0.05 | characteristic barostat response time in ps |
| |
| lang | 0 | flag for running Langevin dynamics |
| langrbuf | 0.0 | radius of Langevin inner buffer sphere |
| langfbeta | 5.0 | friction coefficient for Langevin dynamics |
| langsel | undef | CHARMM atom selection to apply Langevin friction |
| langfile | undef | file for setting friction coefficients |
| langupd | undef | update of Langevin region |
| |
| mcprmc | 0 | turn on MC barostat |
| mctens | 0.0 | MC barostat reference surface tension |
| mcprzz | 1.0 | MC barostat pressure in atm at z dimension |
| mciprsf | 15.0 | MC barostat sampling frequency |
| |
| openmm | 0 | turn on to use openMM |
| |
| |
| |
| |
