[gmx-users] autocorrelation function

[Mark Abraham]

Hi,

No, you'll have to construct that from primitive things. mdrun can write
positions, velocities, forces and "energies."

Mark

On Thu, Aug 27, 2015 at 4:15 PM Sunil Ghimire <ghimiresunil48 at gmail.com>
wrote:

> 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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