VMD-L Mailing List

From: JC Gumbart (gumbart_at_physics.gatech.edu)
Date: Sat Dec 09 2017 - 07:52:15 CST

I was able to reach the source (famed KS graduate Leo Trabuco), who, unsurprisingly, can’t remember why he chose that number seven years ago. :)

If no one has any objections we could change it...

Best,
JC

> On Dec 8, 2017, at 8:16 AM, Peter Jensen Husen <phusen_at_sdu.dk> wrote:
>
> I'm looking at the autoionize.tcl script (v1.25 from vmd-1.9.3), and
> I'm wondering about line 429 for calculating the number of ions:
>
>> set num [expr {int(0.5 + 0.0187 * $saltConcentration * $nWater)}]
>
> so this seems to take the molar mass of water to be 18.7 g/mol, whereas
> I would expect it to be 18.015 g/mol. I also tried to measure the
> density of the pre-equilibrated water box provided by the plugin and
> found 55.5 mol/L as expected. The value 0.00187 in the script would
> correspond to a density of rather 53.5 mol/L.
>
> Surely, it's not a huge error, but I was wondering if there is
> something I am missing? Is the value supposed to be like this (and in
> that case, why?) or is it a mistake?
>
> Best,
> Peter Husen
> Dept. of Physics, Chemistry and Pharmacy
> University of Southern Denmark
>