[gmx-users] autocorrelation function

[Mark Abraham]

The things mdrun can write...

On Thu, Aug 27, 2015 at 5:24 PM Sunil Ghimire <ghimiresunil48 at gmail.com>
wrote:

> primitive things means?
>
> On Thu, Aug 27, 2015 at 8:45 PM, Mark Abraham <mark.j.abraham at gmail.com>
> wrote:
>
> > 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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