1) Algorithm described in paper Impey, R. W.; Madden, P. A.;
McDonald, I.R.J. Chem. Phys. 1983, 87, 5071.
Average time is evaluated between the moment when a atom come into
vicinity of another atom (defined by radius ) until it leave it;
however leaving the shell during time less then “permission time”
(typically 2 ps) not accounted
2) simple average time from the moment when the atom come into
vicinity of another atom (that is within sphere of radius
)
to the moment when it leave, that it will be outside the sphere of radius
3) from exponential decay of conditional probability P(t) for a atom to
remain within a sphere of radius
around given atom if
it enter the sphere of radius
at time t=0 . The exponential
decay of
is evaluated at
Input parameters for this utility follow after the trajectory parameters
in the NAMELIST block RESTIM
:
$RESTIM parameter=value(s), ... $END
The following parameters are used:
NR1 = <value>
number of equivalent sites (first molecule) from which residence time is calculated
IR1 = <i_1>, <i_2>,.... <i_NR1>
sites from which residence time is calculated
NR2 = <value>
number of equivalent sites (second molecule) for which residence time is calculated
IR1 = <i_1>, <i_2>,.... <i_NR1>
sites for which residence time is calculated
NITT = <value>
number of time intervals for computation of residence time
TIMM = <value>
time (in ps) during which probability of leaving hydration shell is calculated
TTER = <value>
“permission time”, in ps, for criteria 3) of the residence time (default 2ps)
RRN = <value>
minimum radius of solvation shell (default 0)
RRX = <value>
radius of hydration shell (recommended to set at the corresponding RDF minimum)
RRD = <value>
“skin” of solvation shell Default: 0.25 Å.
FILOUT = <filename>
name of the output file