Hi Users,
I want to use the isosurface cavity command to look at the cavities available within my structure (a mesoporous silica) to CO2 and other small gaseous molecules. My question is: what should I use as a realistic probe radius? In my modelling I simulate CO2 as below: name epsilon sigma O_CO2 1.10765301 2.9847 C_CO2 0.000 0.000 Is there a formula for determining the probe radius so it can represent the CO2 molecule as my simulation "sees it" i.e using the Lennard Jones parameters? I have seen from some internet searching that water is represented by a probe radius of 1.4. How was this determined? Is there a list of species with their probe radii for Jmol? Also I suppose the envelope will also influence the final result of the cavity search. Is 10 a reasonable value? Thanks Jennifer -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. ------------------------------------------------------------------------- This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
