[gmx-users] Specific heat calculations using gmx energy

[Pragati Sharma]

Thanks, Prof. Spoel. The Enthalpy does make a sudden drop and excluding
that part, the heat capacity values does not differ much with time.
However the values still are far from experimental values ( 7934.66 J/mol
K* compared to ~ 100 *J/mol K). I am using 5.1.1 version, so I cant use the
gmx dos program, it stop with an index error. I will try gmx dos in gromacs
2019 and check the Cp values again.

On Wed, Jul 17, 2019 at 1:04 AM David van der Spoel <spoel at xray.bmc.uu.se>
wrote:

> Den 2019-07-15 kl. 09:24, skrev Pragati Sharma:
> > Dear all,
> >
> > I am simulating a melt of polybutadiene consisting of  60 chains using
> OPLS
> > forcefield. After 50 ns of NPT production run, specific heat is
> calculated
> > using the command:
> >
> > *gmx energy -f ener.edr -fluct_props -nmol 60 -driftcorr *
> > and the value obtained is:
> > Enthalpy                                 =    2010.04 kJ/mol
> > Heat capacity at constant pressure *Cp    =    22807.5 J/mol K*
> >
> > However when I calculate Cp from last 5 ns of trajectory the value is:
> > Enthalpy                                 =    2004.05 kJ/mol
> > Heat capacity at constant pressure *Cp    =    7934.66 J/mol K*
> >
> > Do the Cp calculation is highly dependent on the equilibration of system
> or
> > I am missing something because the experimental valu is ~ 100 *J/mol K,
> *so
> > the values from simulation are also high compared to experiments.
> >
> > *Thanks*
> >
> Did you check whether the enthalpy makes a sudden drop in the beginning
> of the simulation? If so this will influence the fluctuations a lot.
>
> --
> 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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