Manik Mayur wrote:
On Fri, Apr 3, 2009 at 8:25 PM, David van der Spoel
<[email protected] <mailto:[email protected]>> wrote:
Manik Mayur wrote:
Hi,
With reference to
http://www.mail-archive.com/[email protected]/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.
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
[email protected] <mailto:[email protected]>
[email protected] <mailto:[email protected]> 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
[email protected] [email protected] http://folding.bmc.uu.se
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
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