Dear AMBER Developer:
The AMBERtool manual 1.5, describes a command,
set default Dielectric constant (or distance)
I am pretty certain this command does not work. For I have tested with a tleap script file, with that argument set to constant or distance.. it produced exactly the same Parm files in both cases, and the same parm file when I delete that line from the script file. So.. could anyone confirm with me that this command is not valid? (I am using AMBER10)
Also under the next section when you explain eedmeth=5 option under Ewald summation. I would suggest you change the wording there. The distance-dependent dielectric you are using is the following function
epsilon(r)=epsilon_0 * r; (epsilon(r) stands for distance dependent dielectric constant,epsilon_0 is whatever the dielectric constant user specifies). As a result, the electrostatic interaction has 1/r^2 dependence. This function is used for direct part of Columb Interaction. But I am not clear about the long-range part of Coloumb interaction (the part handled by PME). Does PME considers distance-dependent dieletric effect for the long-range electrostatic interaction?
Yongmei Wang
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Received on Wed Sep 14 2011 - 22:00:02 PDT
