Re: [gmx-users] Couette flow

[David van der Spoel]

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>> 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>>> 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
           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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