[gmx-users] Couette flow

[Manik Mayur]

On Fri, Apr 3, 2009 at 8:25 PM, David van der Spoel <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.


>
>
>  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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>>
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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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-- 
Manik Mayur
Graduate student
Microfluidics Lab
Dept. of Mechanical Engg.
IIT Kharagpur
INDIA
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