Tutorial-l Mailing List

From: Frymier, Paul D (pdf_at_utk.edu)
Date: Wed Jan 07 2015 - 14:54:49 CST

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

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