Tutorial-l Mailing List

From: Jeff Comer (jeffcomer_at_gmail.com)
Date: Wed Jan 07 2015 - 15:13:53 CST

You're absolutely right that the way kcal/mol (and kJ/mol) is denoted
in the context of simulations isn't technically consistent. It's
always bothered me too.

The best way to think about it is:

kcal/mol is defined as 1/6.0221413e+23 kcal
kJ/mol is defined as 1/6.0221413e+23 kJ

They both have units of energy (not energy/mole).

It's not really a good definition, but that's what people do.

Jeff

–––––––––––––––––––––––––––––––––––———————
Jeffrey Comer, PhD
Assistant Professor
Institute of Computational Comparative Medicine
Nanotechnology Innovation Center of Kansas State
Kansas State University
Office: P-213 Mosier Hall
Phone: 785-532-6311

On Wed, Jan 7, 2015 at 2:54 PM, Frymier, Paul D <pdf_at_utk.edu> wrote:
> Sorry for the elementary question, but I am stuck. I have searched the
> archives and can’t find the answer to the question(s).
>
>
>
> I am working through the example in the tutorial for computing the heat
> capacity of ubiquitin. I get the following values for the energy from the
> script “average.tcl” using the example files in the common directory for the
> simulation:
>
> <E^2>: 483,089 (assumed units of kcal/mol)
>
> <E>: -693 (same units)
>
>
>
> Using the given equation for cv (cv= (<E^2> - <E>^2)/(kb T^2)), I get a cv
> value of 14.87 kcal/mol-K
>
>
>
> When I attempt to convert this to the units in Table 2 of the NAMD tutorial,
> I am confused by the conversion factor stated of 1 J = 1.43846 x 10^20
> kcal/mol. There should not be mol in the denominator under kcal. Both kcal
> and Joules are units of energy. However, if I simply use the given factor
> and the kb value given (0.00198657 kcal/mol-K) along with the temperature
> (301K) and mass (1.4219 x 10^-23) and arrange the conversion factor so that
> the appropriate units come out on the answer, I get 7,270 J/(kg C) (or K,
> same difference since it will be multiplied by a temperature difference).
> According to information on the web
> (http://www.engineeringtoolbox.com/human-body-specific-heat-d_393.html), the
> Cv for proteins should be around 1700 J/kg-C or so.
>
>
>
> So I then tried to convert the units using the molecular mass of ubiquitin
> (8.5 kD) and the actual conversion between kcal and J (4184 J/kcal), I got a
> value that was even further off.
>
>
>
> I am clearly missing something simple. Any help is much appreciated.
>
>
>
> Paul Frymier
>
> Associate Professor
>
> Department of Chemical and Biomolecular Engineering
>
> University of Tennessee, Knoxville
>
> 419 Dougherty Engineering Building
>
> Knoxville, TN 37996-2200
>
> Office: (865)-974-4961
>
> Fax: (865)-974-7076
>
>

**
** Visit http://www.greatcircle.com/majordomo/ for more info on majordomo
**