On Fri, Apr 3, 2009 at 8:25 PM, David van der Spoel <[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. > > > 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 >> >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> gmx-users mailing list [email protected] >> http://www.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/search before >> posting! >> Please don't post (un)subscribe requests to the list. Use the www >> interface or send it to [email protected]. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> > > > -- > 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 > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ > _______________________________________________ > gmx-users mailing list [email protected] > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to [email protected]. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Manik Mayur Graduate student Microfluidics Lab Dept. of Mechanical Engg. IIT Kharagpur INDIA
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