next up previous contents
Next: Time correlation functions: trtcf.f Up: Tranal utility Previous: Ramachandran plot for a   Contents

Residence time calculation: restime.f

This utility computes residence time of a molecule (atom) to be within a given distance ($R_{hyd}$) around another atom (of another molecule). The program computes residence time according to three somewhat different definitions:

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 $R_{hyd}$) until it leave it; however leaving the shell during time less then ``permission time'' $t_{per}$ (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 $R_{hyd}-\delta r$) to the moment when it leave, that it will be outside the sphere of radius $R_{hyd}+\delta r$

3) from exponential decay of conditional probability P(t) for a atom to remain within a sphere of radius $R_{hyd}+\delta r$ around given atom if it enter the sphere of radius $R_{hyd}-\delta r$ at time t=0 . The exponential decay of $P(t)$ is evaluated at $t < t_{per}$

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:


next up previous contents
Next: Time correlation functions: trtcf.f Up: Tranal utility Previous: Ramachandran plot for a   Contents
Alexander Lyubartsev 2015-02-06