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t_UmbrellaOptions Struct Reference
+ Collaboration diagram for t_UmbrellaOptions:

Description

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 * fnPdo
 
const char * fnPullx
 file names of input
 
gmx_bool bTpr
 
gmx_bool bPullf
 
gmx_bool bPdo
 
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_coordselectioncoordsel
 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 interations
 
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: