[gmx-users] Heat capacity calculations from fluctuations and using g_dos

Srinath Kompella srinathkompella2910 at gmail.com
Fri Jan 12 07:51:14 CET 2018

Dear David,
                   Thank you for the response. I'll perform simulations as
per your suggestions and see if I'll get more accurate heat capacity values.

                   Thank you.

On Thu, Jan 11, 2018 at 12:46 AM, David van der Spoel <spoel at xray.bmc.uu.se>

> Den 2018-01-10 kl. 09:04, skrev Srinath Kompella:
>> Hello all,
>>                I've simulated Methylcyclohexane (MCH) in NVT and NPT
>> ensembles using GROMACS-5.1.4, from which I want to calculate the heat
>> capacities (Cv and Cp respectively) of MCH. If I use the fluctuation
>> properties, I get the following note: "Heat capacities obtained from
>> fluctuations do *not* include quantum corrections. If you want to get a
>> more accurate estimate, please use the g_dos program." After going through
>> a few discussions on GROMACS mailing lists, I used "gmx dos" module
>> thinking that I would get the quantum corrections for the heat capacities.
>> But the heat capacity values written at the end of the "dos.log" are
>> larger
>> than that of those calculated using fluctuation properties.
>> *Temperature(K)                             Cv (J/mol K)
>>                            Cp (J/mol K)              *
>>                                  *Fluctuation Properties          g_dos  *
>>          *Fluctuation Properties        g_dos  *
>>         298.15                            165.564                 275.747
>>                   193.939                  274.531
>>                I noticed that the numbers fluctuation properties give are
>> relatively much closer to the experimental values.
>>                Please help me understand why the numbers are very
>> different
>> and which method to go for. Thank you in advance.
>> Correspondence to experiment is not a way to check your results.
> In order for the corrections to work you need to perform a 100 ps NVT
> simulation saving velocities and positions every 4-5 fs and without using
> constraints.
> --
> David van der Spoel, Ph.D., Professor of Biology
> Head of Department, Cell & Molecular Biology, Uppsala University.
> Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
> http://www.icm.uu.se
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Srinath Kompella
Ph.D. Research Scholar
Molecular Simulations Laboratory,
Chemistry and Physics of Materials Unit (CPMU),
Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR),
Jakkur - 560 064, Bangalore,
Karnataka State, India.

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