[gmx-users] Thermal Conductivity

Diego Vallejo DiegoVallejo at mdq.com.ar
Tue Jul 23 21:31:50 CEST 2002


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.
> 





More information about the gromacs.org_gmx-users mailing list