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UmbrellaOptions Struct Reference
+ 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
 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

The documentation for this struct was generated from the following file: