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...
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] [email protected] http://folding.bmc.uu.se
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