Gromacs
2024.4
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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 |