On Fri, Apr 3, 2009 at 11:11 PM, David van der Spoel <[email protected]>wrote:
> Manik Mayur wrote: > >> >> >> On Fri, Apr 3, 2009 at 10:47 PM, David van der Spoel < >> [email protected] <mailto:[email protected]>> wrote: >> >> Manik Mayur wrote: >> >> >> >> On Fri, Apr 3, 2009 at 9:48 PM, David van der Spoel >> <[email protected] <mailto:[email protected]> >> <mailto:[email protected] <mailto:[email protected]>>> >> wrote: >> >> Manik Mayur wrote: >> >> >> >> On Fri, Apr 3, 2009 at 8:25 PM, David van der Spoel >> <[email protected] <mailto:[email protected]> >> <mailto:[email protected] <mailto:[email protected]>> >> <mailto:[email protected] >> <mailto:[email protected]> <mailto:[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. >> >> >> 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. >> >> if (g == 0) >> APPLy acceleration >> else if (g == 1) >> apply velocity >> else >> do normal update >> >> I really appreciate your help. One last doubt, what is this 'g' or the >> group you are talking about? As we define acc_grps by their names and not >> numbers in the mdp file. Do we have to introduce some new parameter 'g' >> which will be defined as 0 or 1 accordingly? >> > EasY: > > acc_groups = Cucumber TOmata > means Cucumber = 0, Tomato = 1 > Got it. :) Thanks a lot. >> Also, can't we have this feature in the main stream GROMACS rather than >> having our own custom build, something like vel_grps? Just a suggestion. >> > Sure, but that doesn't help you now. > Yes, but I would like to see my favorite MD package as one of the most versatile package available :) >> Thanks, >> >> >> >> 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] >> <mailto:[email protected]> >> <mailto:[email protected] <mailto:[email protected] >> >> >> <mailto:[email protected] >> <mailto:[email protected]> <mailto:[email protected] >> <mailto:[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] <mailto: >> [email protected]> >> <mailto:[email protected] >> <mailto:[email protected]>> >> <mailto:[email protected] >> <mailto:[email protected]> >> <mailto:[email protected] >> <mailto:[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] <mailto:[email protected]> >> <mailto:[email protected] <mailto:[email protected]>> >> <mailto:[email protected] >> <mailto:[email protected]> <mailto:[email protected] >> <mailto:[email protected]>>> [email protected] >> <mailto:[email protected]> <mailto:[email protected] >> <mailto:[email protected]>> >> <mailto:[email protected] <mailto:[email protected]> >> <mailto:[email protected] <mailto:[email protected]>>> >> http://folding.bmc.uu.se >> >> >> >> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ >> _______________________________________________ >> gmx-users mailing list [email protected] >> <mailto:[email protected]> >> <mailto:[email protected] <mailto:[email protected] >> >> >> <mailto:[email protected] >> <mailto:[email protected]> <mailto:[email protected] >> <mailto:[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] >> <mailto:[email protected]> >> <mailto:[email protected] >> <mailto:[email protected]>> >> <mailto:[email protected] >> <mailto:[email protected]> >> <mailto:[email protected] >> <mailto:[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 >> >> >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> gmx-users mailing list [email protected] >> <mailto:[email protected]> >> <mailto:[email protected] <mailto:[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] >> <mailto:[email protected]> >> <mailto:[email protected] >> <mailto:[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] <mailto:[email protected]> >> <mailto:[email protected] <mailto:[email protected]>> >> [email protected] <mailto:[email protected]> >> <mailto:[email protected] <mailto:[email protected]>> >> http://folding.bmc.uu.se >> >> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ >> _______________________________________________ >> gmx-users mailing list [email protected] >> <mailto:[email protected]> >> <mailto:[email protected] <mailto:[email protected]>> >> http://www.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/searchbefore >> posting! >> Please don't post (un)subscribe requests to the list. Use the >> www >> interface or send it to [email protected] >> <mailto:[email protected]> >> <mailto:[email protected] >> <mailto:[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 >> >> >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> gmx-users mailing list [email protected] >> <mailto:[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] >> <mailto:[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] <mailto:[email protected]> >> [email protected] <mailto:[email protected]> http://folding.bmc.uu.se >> >> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ >> _______________________________________________ >> gmx-users mailing list [email protected] >> <mailto:[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] >> <mailto:[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 >> >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> 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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