[gmx-users] specific heat

[David van der Spoel]

On 2011-01-30 11.43, leila separdar wrote:
>
> is there any command in gromacs that gives me a list of data points for
> specific heat and suseptibility as a function of temperature or time ?
> if not, then how can i calculate specific heat or polt Cv as a fuction of T?
>
This is not trivial. You can compute the specific heat from fluctuations 
in the enthalpy or total energy:

cP = (<H^2> - <H>^2)/kB T^2 (NPT sim)

cV = (<Etot^2> - <Etot>^2)/kB T^2 (NVT sim)

In addition you need to apply quantum corrections which are not 
negligible (see manual chapter 1). You can do this using a normal mode 
analysis.

The implementation in released versions of g_energy is not correct, but 
as it happens I just committed a new version of g_energy and g_nmeig. If 
you download gromacs from git and checkout the release-4-5-patches 
branch everything should be there to compute cP/cV. Run g_nmeig -h for 
more information.

As regards susceptibility, do you mean the dielectric constant? That can 
be computed using g_dipoles *from a trajectory* - not from an energy 
file anymore.
-- 
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