[gmx-users] Heat capacity for infinite systems

[David]

On Thu, 2004-08-26 at 00:02, Chris O'Brien wrote:
> Dear gmx-users,
> 
> I am simulating a system of 32 infinite (pbc=full) crystalline polymer 
> chains, and I am wondering what basis g_energy uses for its calculation of 
> the heat capacity.  I obtain a value of 12.5 J/mol/K, and I would like to 
> compare it to a literature value with units of J/kg/K but I am not sure how 
> to make the conversion.  What role (if any) does the option -nmol play in 
> the calculation of Cv?
This is crucial, however for polymers the definition of a molecule maybe
not so clear (but that's your problem). For small molecules you need to
add this.

The equations for Cv come from Allen and TIldesley and are based on the
fluctuation of the temperature. If you have Berendsen coupling your
fluctuations are damped and you will get a too low Cv. If you have
Nose-Hoover coupling you have other artefacts. Best is to measure
without T coupling.
> 
> Also, what does the (factor = xxxxx) indicate after the value of the heat 
> capacity?
IIRC that's an intermediate result. Forget it. Of course you can check
the source code.
> 
> Thank you,
> 
> Chris O'Brien
> 
> Department of Chemical Engineering
> Clemson University
> Clemson, SC  29634-0909
> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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