[gmx-users] Thermal Conductivity

[Markus O Kaukonen]

Dear Diego & al,

See

http://www.mpip-mainz.mpg.de/documents/projects98/B8.htm

and

F. Müller-Plathe: "A Simple Non-equilibrium Molecular Dynamics Method
for Calculating the Thermal Conductivity", J. Chem. Phys. 106 (1997)
6082-6085.

This should be simple to code and understand.

Best Wishes, Markus

ps. Sorry for the late comment,
    July is in practice a public holiday here up in the north.


On Tue, 23 Jul 2002, Diego Vallejo wrote:

> Hola:
>
> Any of you know about code to compute the Thermal Conductivity?
> I didn't see this in Gromacs...
>
> 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.
>
>
> BTW, d'u know how can I read the coordinates directly from fortran?
> I mean, directly from the trr files
>
> Saludos
>
> Diego
> Diego Vallejo
> diegovallejo at mdq.com.ar
>
>
> -----Original Message-----
> From: Marcos Villarreal <arloa at dqb.fcq.unc.edu.ar>
> To: "J Simms" <JXS818 at bham.ac.uk>
> Date: Mon, 22 Jul 2002 14:27:51 -0300
> Subject: Re: [gmx-users] How to make a TM protein - Help
>
> >
> > Dear John,
> >
> > Here is a simple protocol to make a hole in a membrane.
> > 1) take an equilibrated membrane and remove the water and some lipids
> > in the
> > center. If your helix has an cross molecular area of about 1.5 nm^2
> > you
> > should remove 2 dppc per monolayer (area 0.64 nm^2)
> > 2) manually insert in the pdb a "string" of atoms called XXX (fig 1)
> > 3) link the XXX atoms by bonds and define a repulsive interaction
> > with the
> > rest of the atoms in your system.(xxx.itp)
> > 4) minimize and perform a series of MD with position restrains in the
> > XXX
> > atoms and gradually increasing the repulsive force .
> >
> > Some tricks:
> > -You should probably have to move some torsion angles in some lipids
> > chains
> > before you can get a "clear path" where to put the XXX atoms. This
> > can be
> > done with rasmol (settings-> pick bond; settings ->rotate bond)
> > -In the first MD you should probably have to use a short timestep
> > (0.5 fs)
> > and low temperature (100K).
> > -Use PBC, NVT and don't go beyond about 200 ps in total (in step 4)
> > because
> > the rest of the membrane could be deformed.
> > -Once you get a fine hole, put back the water molecules. Equilibrate
> > them an
> > perform some annealing in the lipid chains. ie put the lipids at 450K
> > while
> > the water stay at 330K or something like this. Then cool down the
> > lipids
> > gradually. This step is important to remove some possible bad lipid
> > chains
> > conformation.
> > -you are ready to insert you peptide in the system.
> >
> > I hope this can help you.
> > Saludos,
> > --
> > Marcos Villarreal
> > Grupo de Biofisica
> > Departamento de Quimica Biologica - CIQUIBIC.
> > Universidad Nacional de Cordoba.
> > Cordoba. Argentina.
> >
> > -------------------------------------------------------
> >
> > --
> > Marcos Villarreal
> > Grupo de Biofisica
> > Departamento de Quimica Biologica - CIQUIBIC.
> > Universidad Nacional de Cordoba.
> > Cordoba. Argentina.
> >
>
>
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