[gmx-users] Couette flow
David van der Spoel
spoel at xray.bmc.uu.se
Fri Apr 3 19:17:37 CEST 2009
Manik Mayur wrote:
>
>
> On Fri, Apr 3, 2009 at 9:48 PM, David van der Spoel
> <spoel at xray.bmc.uu.se <mailto:spoel at xray.bmc.uu.se>> wrote:
>
> 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>
> <mailto: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.
>
>
> Can you provide more insight on how to achieve it, as from your
> suggestion it turns out, I can have either constant velocity build of
> GROMACS or the constant acceleration one.
if (g == 0)
APPLy acceleration
else if (g == 1)
apply velocity
else
do normal update
>
>
>
>
>
> 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>
> <mailto:spoel at xray.bmc.uu.se <mailto:spoel at xray.bmc.uu.se>>
> spoel at gromacs.org <mailto:spoel at gromacs.org>
> <mailto: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 <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
>
>
> ------------------------------------------------------------------------
>
> _______________________________________________
> gmx-users mailing list gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
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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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