On Fri, Apr 3, 2009 at 9:48 PM, David van der Spoel <sp...@xray.bmc.uu.se>wrote:
> Manik Mayur wrote: > >> >> >> On Fri, Apr 3, 2009 at 8:25 PM, David van der Spoel >> <sp...@xray.bmc.uu.se<mailto: >> sp...@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. > >> >> >> 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 gmx-users@gromacs.org >> <mailto:gmx-users@gromacs.org> >> 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 gmx-users-requ...@gromacs.org >> <mailto:gmx-users-requ...@gromacs.org>. >> 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 >> sp...@xray.bmc.uu.se <mailto:sp...@xray.bmc.uu.se> >> sp...@gromacs.org <mailto:sp...@gromacs.org> http://folding.bmc.uu.se >> >> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ >> _______________________________________________ >> gmx-users mailing list gmx-users@gromacs.org >> <mailto:gmx-users@gromacs.org> >> 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 gmx-users-requ...@gromacs.org >> <mailto:gmx-users-requ...@gromacs.org>. >> 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 >> >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> gmx-users mailing list gmx-users@gromacs.org >> 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 gmx-users-requ...@gromacs.org. >> 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 > sp...@xray.bmc.uu.se sp...@gromacs.org http://folding.bmc.uu.se > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > 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 gmx-users-requ...@gromacs.org. > 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
_______________________________________________ gmx-users mailing list gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
