[gmx-users] Read Coordinates

[K.A. Feenstra]

Nestor Sanchez Fornillo wrote:
> 
> Mensaje citado por: Diego Vallejo
> <DiegoVallejo at mdq.com.ar>:
> 
> > Hola:
> >
> > Any of you know about code to compute the Thermal Conductivity?
> > I didn't see this in Gromacs...

Right. It isn't there (yet?).

> > As far as I know this is obtained like the Self Diffusion Constant
> > via a Green-Kubo Relation or an equivalent Einstein Relation.
> > Instead of taking velocities into account you have to do it with
> > energies.

Hmm. That sounds like you will need energies per atom or per molecule,
or perhaps per coordinate. These are not readily available, and I am
actually unsure if it is even possible to calculate them based on
atom-pair interaction energies (which are, basically, the only real
energies that are used; all others are derived from this).

> > BTW, d'u know how can I read the coordinates directly from fortran?
> > I mean, directly from the trr files
> 
> Yes, check gmxdump at
> http://www.gromacs.org/documentation/reference_3.0/onlin
> e/gmxdump.html

I would rather think Diego had the possibility of using direct
library calls from the fortran code. I've heard at least one
person describe on the mailing list the problems he had while 
implementing this for one of his own programs. If you search
back in the archive for e.g. fortran and trajectory, you will
probably find it...

--Groetjes,

Anton.