|
Gromacs
2025-dev-20241003-bd59e46
|
All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Macros Groups Pages
|
Gromacs
2025-dev-20241003-bd59e46
|
Collaboration diagram for UmbrellaOptions:Parameters of WHAM.
Public Attributes | |
| gmx::DefaultRandomEngine | rng |
| gromacs random number generator | |
| gmx::TabulatedNormalDistribution | normalDistribution |
| Uses default: real output, 14-bit table. | |
Input stuff | |
| const char * | fnTpr |
| const char * | fnPullf |
| const char * | fnCoordSel |
| const char * | fnPullx |
| file names of input | |
| gmx_bool | bPullf |
| gmx_bool | bPullx |
| input file types given? | |
| real | tmin |
| real | tmax |
| real | dt |
| only read input within tmin and tmax with dt | |
| gmx_bool | bInitPotByIntegration |
| before WHAM, guess potential by force integration. Yields 1.5 to 2 times faster convergence | |
| int | stepUpdateContrib |
| update contribution table every ... iterations. Accelerates WHAM. | |
| int | nCoordsel |
| if >0: use only certain group in WHAM, if ==0: use all groups | |
| t_coordselection * | coordsel |
| for each tpr file: which pull coordinates to use in WHAM? | |
Basic WHAM options | |
| int | bins |
| nr of bins, min, max, and dz of profile | |
| real | min |
| real | max |
| real | dz |
| real | Temperature |
| real | Tolerance |
| temperature, converged when probability changes less than Tolerance | |
| gmx_bool | bCycl |
| generate cyclic (periodic) PMF | |
Output control | |
| gmx_bool | bLog |
| energy output (instead of probability) for profile | |
| int | unit |
| unit for PMF output kJ/mol or kT or kCal/mol | |
| gmx_bool | bSym |
| symmetrize PMF around z=0 after WHAM, useful for membranes etc. | |
| real | zProf0 |
| after wham, set prof to zero at this z-position. When bootstrapping, set zProf0 to a "stable" reference position. | |
| gmx_bool | bProf0Set |
| setting profile to 0 at zProf0? | |
| gmx_bool | bBoundsOnly |
| gmx_bool | bHistOnly |
| determine min and max, or write histograms and exit | |
| gmx_bool | bAuto |
| determine min and max automatically but do not exit | |
| gmx_bool | verbose |
| more noisy wham mode | |
| int | stepchange |
| print maximum change in prof after how many interactions | |
| gmx_output_env_t * | oenv |
| xvgr options | |
Autocorrelation stuff | |
| gmx_bool | bTauIntGiven |
| gmx_bool | bCalcTauInt |
| IACT given or should be calculated? | |
| real | sigSmoothIact |
| sigma of Gaussian to smooth ACTs | |
| gmx_bool | bAllowReduceIact |
| Allow to reduce ACTs during smoothing. Otherwise ACT are only increased during smoothing. | |
| real | acTrestart |
| when computing ACT, time between restarting points | |
| gmx_bool | bHistEq |
Bootstrapping stuff | |
| int | nBootStrap |
| nr of bootstraps (50 is usually enough) | |
| int | bsMethod |
| real | tauBootStrap |
| int | histBootStrapBlockLength |
| int | bsSeed |
| random seed for bootstrapping | |
| gmx_bool | bs_verbose |
tabulated umbrella potential stuff | |
| gmx_bool | bTab |
| double * | tabX |
| double * | tabY |
| double | tabMin |
| double | tabMax |
| double | tabDz |
| int | tabNbins |
1.8.5