[gmx-users] Couette flow

David van der Spoel spoel at xray.bmc.uu.se
Fri Apr 3 19:41:44 CEST 2009


Manik Mayur wrote:
> 
> 
> On Fri, Apr 3, 2009 at 10:47 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 9:48 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:
> 
> 
> 
>                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>>
>                <mailto: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?
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
>                   spoel at xray.bmc.uu.se <mailto:spoel at 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
>            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
> 
> 
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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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