[gmx-users] heat capacity in 4.5.3 and 4.0.7

[David van der Spoel]

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
> correct?
>
>
>         Many thanks for you time!
>         Best,
>
>


-- 
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