VMD-L Mailing List

From: Peter Jensen Husen (phusen_at_sdu.dk)
Date: Mon Dec 18 2017 - 03:26:09 CST

Well, I don't know if that should be my say (I don't have objections). I'm just doing something similar myself, and I wanted to know, if I was missing something very clever, that I should also take into account.

Best, Peter


On Sat, 2017-12-09 at 08:52 -0500, JC Gumbart wrote:

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<mailto: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