Re: [gmx-users] Couette flow

[David van der Spoel]

Manik Mayur wrote:


On Fri, Apr 3, 2009 at 10:47 PM, David van der Spoel 
<sp...@xray.bmc.uu.se <mailto:sp...@xray.bmc.uu.se>> wrote:

    Manik Mayur wrote:



        On Fri, Apr 3, 2009 at 9:48 PM, David van der Spoel
        <sp...@xray.bmc.uu.se <mailto:sp...@xray.bmc.uu.se>
        <mailto:sp...@xray.bmc.uu.se <mailto:sp...@xray.bmc.uu.se>>> wrote:

           Manik Mayur wrote:



               On Fri, Apr 3, 2009 at 8:25 PM, David van der Spoel
               <sp...@xray.bmc.uu.se <mailto:sp...@xray.bmc.uu.se>
        <mailto:sp...@xray.bmc.uu.se <mailto:sp...@xray.bmc.uu.se>>
               <mailto:sp...@xray.bmc.uu.se
        <mailto:sp...@xray.bmc.uu.se> <mailto:sp...@xray.bmc.uu.se
        <mailto:sp...@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?
EasY:

acc_groups = Cucumber TOmata
means Cucumber = 0, Tomato = 1


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.
Sure, but that doesn't help you now.


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
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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
           sp...@xray.bmc.uu.se <mailto:sp...@xray.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
    sp...@xray.bmc.uu.se <mailto:sp...@xray.bmc.uu.se>  
     sp...@gromacs.org <mailto:sp...@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
sp...@xray.bmc.uu.se    sp...@gromacs.org   http://folding.bmc.uu.se
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