[gmx-users] Couette flow

[David van der Spoel]

Manik Mayur wrote:
> 
> 
> On Fri, Apr 3, 2009 at 8:25 PM, David van der Spoel 
> <spoel at xray.bmc.uu.se <mailto:spoel at xray.bmc.uu.se>> wrote:
> 
>     Manik Mayur wrote:
> 
>         Hi,
> 
>         With reference to
> 
>         http://www.mail-archive.com/gmx-users@gromacs.org/msg13374.html
> 
>         I would like to know if anybody has successfully simulated
>         couette flow using GROMACS. If yes, then please suggest what
>         specific steps has to be taken. If no, then are the developers
>         planning to implement giving constant velocity to a group of
>         atoms, as we can do in LAMMPS, in future versions.
> 
>         It will really be a life saver if GROMACS can be used for such
>         problems.
> 
> 
>     As the mail you pointed to suggest, it is quite simple to do
>     yourself. As a first guess look for routine
>     static void do_update_md(int start,int homenr,double dt,
> 
>     in src/mdlib/update.c
> 
>     and find this line:
> 
>              /* do not scale the mean velocities u */
>              vn             = gstat[ga].u[d] + accel[ga][d]*dt + vnrel;
> 
>     and replace it by
> 
>              /* do not scale the mean velocities u */
>              vn             = gstat[ga].u[d] + accel[ga][d] + vnrel;
> 
>     and recompile.
> 
>     As you see, I just removed the multiplication by the time step. Now
>     in the input file (mdp) you enter the velocity instead of the
>     acceleration in the appropriate entries, and you are good to go. You
>     may need to remove the mean velocity of the group as well...
> 
> 
> Thanks a lot for the suggestion. But will this work if I have 2 groups, 
> one with constant velocity and another with constant acceleration? Like 
> a superposition of couette and poiseuille flow.
You didn't mention that :(.
No, you will have to do some more hacking, but you could e.g. make group 
0 to have acceleration and group 1 a velocity.


>  
> 
> 
> 
>         Also can we build GROMACS as a library to be called from
>         customized codes?
> 
>         Thanks,
>         -- 
>         Manik Mayur
>         Graduate student
>         Microfluidics Lab
>         Dept. of Mechanical Engg.
>         IIT Kharagpur
>         INDIA
> 
> 
>         ------------------------------------------------------------------------
> 
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> 
> 
>     -- 
>     David.
>     ________________________________________________________________________
>     David van der Spoel, PhD, Professor of Biology
>     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 <mailto:spoel at xray.bmc.uu.se>  
>      spoel at gromacs.org <mailto:spoel at gromacs.org>   http://folding.bmc.uu.se
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> 
> 
> 
> 
> -- 
> Manik Mayur
> Graduate student
> Microfluidics Lab
> Dept. of Mechanical Engg.
> IIT Kharagpur
> INDIA
> 
> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Professor of Biology
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://folding.bmc.uu.se
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