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.
sp...@xray.bmc.uu.se http://folding.bmc.uu.se
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