[gmx-users] selective temperature coupling

Berk Hess gmx3 at hotmail.com
Tue Apr 26 16:32:44 CEST 2005

>From: Stephan Dammer <S.M.Dammer at tnw.utwente.nl>
>Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>To: gmx-users at gromacs.org
>Subject: [gmx-users] selective temperature coupling
>Date: Tue, 26 Apr 2005 16:16:05 +0200 (CEST)
>I would like to do some NEMD-simulations of flow of a LJ-fluid between
>two parallel solid walls. Usually in such simulations, one does not couple
>all velocity components of the fluid to a heat bath but only that which is
>perpendicular to the flow. As far as I understand, that feature is not
>included in GROMACS. Hence, it would need some modification of the code to
>couple, let's say, only the y-coordinate to a heat bath (e.g., by Langevin
>dynamics) and not the x and z component. Could you perhaps give me a hint,
>where the best location would be for such a modification (update.c?).
>Since such flow simulations are becoming more popular, it might be
>interesting for the developers to include something like this in a future
>version of GROMACS.

With stochastic dynamics this is very easy to implement (also because
you do not need to change the temperature calculation).
You can simple remove the fricion and noise from the components
you want in do_update_sd in update.c


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