[gmx-users] RE: NEMD

[David van der Spoel]

Junfang.Zhang at csiro.au wrote:

>Hi David,
>
>Thank you very much for your reply.
>
>I am going to be involved in two research projects, gas hydrates and
>clay swelling, by using Gromacs.
>
>As I am new user of Gromacs, I am wondering if you can give me some
>advice on the following questions:
>
>Non-equilibrium MD (NEMD) simulation of clay swelling:  two-half
>negatively charged clay layer in the simulation box, which is fixed.
>Water molecules and cations between the clay layers will flow. Can you
>please let me know how to perform non-equilibrium MD simulation by using
>Gromacs? Where to specify the parameters for NEMD?
>
>As the external force will be introduced, the viscous heat should be
>removed from the system. Since the clay layers are fixed, do I have to
>thermostat the fluids between the walls?
>  
>
I'm not sure I understand what you mean with external force, but you can 
add external accelerations by specifying acceleration groups in the mdp 
file. You should definitely thermostat the groups separately.


-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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