[gmx-users] autocorrelation function

[Sunil Ghimire]

Dear sir,
 Thanks for suggestion.

Is it possible to write heat current vector j in trr file ( by using
suitable mdp file) so that we may extract it to find heat current
autocorrelation ?  Because, I need heat  current autocorrelation to
calculate the thermal conductivity.

On Thu, Aug 27, 2015 at 7:34 PM, gozde ergin <gozdeeergin at gmail.com> wrote:

> I am trying to estimate the autocorrelation of force.
> To do that I need the get the time series of *the total bath force acting
> on a molecule and this molecule is the pulled molecule that I use for
> umbrella sampling*.
> What is the difference between total bath force acting on a molecule and
> sum of the forces of each atom on the system?
> I got confuse about this term.
> I know I can get the time series of total force by using g_traj and than
> g_analyze give me the autocorrelation.
>
>
>
> On Thu, Aug 27, 2015 at 8:59 AM, Mark Abraham <mark.j.abraham at gmail.com>
> wrote:
>
> > Hi,
> >
> > Get the time series, and then use your favourite numerical analysis
> package
> > (or gmx analyze).
> >
> > Mark
> >
> > On Thu, Aug 27, 2015 at 5:33 AM Sunil Ghimire <ghimiresunil48 at gmail.com>
> > wrote:
> >
> > > Dear sir ,
> > >         How can we compute the autocorrelation function of the
> > temperature
> > > or kinetic energy ? I want to calculate thermal conductivity of noble
> > gases
> > > from green - kubo formalism.
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