[gmx-users] Couette flow
Manik Mayur
manik.mayur at gmail.com
Fri Apr 3 19:37:56 CEST 2009
On Fri, Apr 3, 2009 at 10:47 PM, David van der Spoel
<spoel at xray.bmc.uu.se>wrote:
> 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
>
>>
I really appreciate your help. One last doubt, what is this 'g' or the group
you are talking about? As we define acc_grps by their names and not numbers
in the mdp file. Do we have to introduce some new parameter 'g' which will
be defined as 0 or 1 accordingly?
Also, can't we have this feature in the main stream GROMACS rather than
having our own custom build, something like vel_grps? Just a suggestion.
Thanks,
>>
>>
>> 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
>>
>>
>>
>> ------------------------------------------------------------------------
>>
>> _______________________________________________
>> gmx-users mailing list gmx-users at gromacs.org
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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
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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
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> _______________________________________________
> gmx-users mailing list gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
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>
--
Manik Mayur
Graduate student
Microfluidics Lab
Dept. of Mechanical Engg.
IIT Kharagpur
INDIA
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