[gmx-users] RE: NEMD

David van der Spoel spoel at xray.bmc.uu.se
Fri Dec 2 09:01:03 CET 2005

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 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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