[gmx-users] heat capacity in 4.5.3 and 4.0.7
David van der Spoel
spoel at xray.bmc.uu.se
Sun Mar 27 21:09:39 CEST 2011
On 2011-03-27 19.23, Elisabeth wrote:
> Thanks David for replying me. I appreciate your attention to
> comment on the following short inquiries.
> 1- g_energy says:
> you will need to give the number of constraints per molecule
> –nconstr and
> for water this is 3. Can you elaborate on how to set this option. When
> constraints= all-bonds how to set -nconstr for a simlpe alkane for
> instance? It refers to number of atoms of each molecule on which
> constraints are applied?
Sorry but you have to do it yourself. Look up the equations and extract
the numbers from the energy file.
The other parameters may be problematic too.
> 2- Aside from heat capacities, does g_energy report the
> following properties correctly?
> Thermal expansion coeff. (NPT): Enthalpy, Vol, Temp
> Isothermal compressibility: Vol, Temp
> Adiabatic bulk modulus: Vol, Temp
> 3- Since volume appears for calculation of the above properties
> , does this imply ONLY NPT results in these properties? (because
> in NPT g_energy reports "volume").
> 4- For thermal expansion: I read one of your earlier messages
> saying that enthalpy = Etot(total energy) +pv, [where Etot is
> potential+kinetic (in g_energy list)]
> and for pv , take ref_p and not measure p (that g_energy
> reports). If the system is equilibrated to ref_p, then why not taking pv
> from g_energy? you mean product of pv that g_energy gives is not
> Many thanks for you time!
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
spoel at xray.bmc.uu.se http://folding.bmc.uu.se
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