[gmx-users] autocorrelation function

[Sunil Ghimire]

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.
> > > > > --
> > > > > Gromacs Users mailing list
> > > > >
> > > > > * Please search the archive at
> > > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > > > posting!
> > > > >
> > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > > > >
> > > > > * For (un)subscribe requests visit
> > > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> > or
> > > > > send a mail to gmx-users-request at gromacs.org.
> > > > >
> > > > --
> > > > Gromacs Users mailing list
> > > >
> > > > * Please search the archive at
> > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > > posting!
> > > >
> > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > > >
> > > > * For (un)subscribe requests visit
> > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> or
> > > > send a mail to gmx-users-request at gromacs.org.
> > > >
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at
> > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > posting!
> > >
> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >
> > > * For (un)subscribe requests visit
> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > > send a mail to gmx-users-request at gromacs.org.
> > >
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>