Well..they do move forward for a few ps and then they move back (they oscillate). Did you check for a longer period?
Alex Berk Hess schrieb: > Strange... > I tested the code on the files you sent me > and the slabs were moving smoothly. > > Berk > > > Date: Mon, 28 Sep 2009 15:40:16 +0200 > > From: alexander.h...@mytum.de > > To: gmx-users@gromacs.org > > Subject: Re: [gmx-users] direction_periodic > > > > Hey, > > > > so using the new direction_periodic with some kernels that actually work > > and the sources from the git (unmodified) > > gives a nice smooth pull force but no actual mean displacement of the > > groups to be pulled (on average they just stay where they are,see > > attached graph). I'm still trying to pull them into opposite directions > > though. > > > > I'm using this setup: > > pull = umbrella > > pull_geometry = direction_periodic > > pull_ngroups = 1 > > pull_group0 = DIAM > > pull_group1 = DIAM2 > > pulldim = Y N N > > pull_k1 = 1000.0 > > pull_rate1 = 0.01 > > pull_vec1 = -1.0 0.0 0.0 > > > > How can I make the two diamond slabs actually move in opposite > > directions rather than just oscillating around their > > initial positions? > > > > Thx, > > Alex > > > > Berk Hess schrieb: > > > Hi, > > > > > > Don't use fortran. > > > We will get rid of it before the 4.1 release. > > > > > > Berk > > > > > > > Date: Mon, 21 Sep 2009 16:17:17 +0200 > > > > From: alexander.h...@mytum.de > > > > To: gmx-users@gromacs.org > > > > Subject: Re: [gmx-users] direction_periodic > > > > > > > > Hey, > > > > > > > > ok, I checked this. It works ok with the assembly kernels on my > local > > > > machine, but it fails with fortran kernels > > > > on the HPC and on my local machine. > > > > > > > > Alex > > > > > > > > Berk Hess schrieb: > > > > > Yes. > > > > > > > > > > Berk > > > > > > > > > > > Date: Mon, 21 Sep 2009 14:42:43 +0200 > > > > > > From: alexander.h...@mytum.de > > > > > > To: gmx-users@gromacs.org > > > > > > Subject: Re: [gmx-users] direction_periodic > > > > > > > > > > > > With master branch you mean the code I get via > > > > > > > > > > > > |git clone git://git.gromacs.org/gromacs.git > > > > > > > > > > > > right? > > > > > > > > > > > > Alex > > > > > > | > > > > > > > > > > > > > > > > > > > > > > > > Berk Hess schrieb: > > > > > > > I tested on your system and got good results. > > > > > > > There is still a tricky issue: the pull COM is still > determined > > > > > > > in the "standard" way by summing distances from the pbcatom. > > > > > > > Therefore atoms should not change nearest image from he > pbcatom. > > > > > > > This would result in nasty noise in the pull COM and force. > > > > > > > > > > > > > > I would suggest that you try to run the master branch and > check > > > > > > > if that works. > > > > > > > > > > > > > > Berk > > > > > > > > > > > > > > > Date: Mon, 21 Sep 2009 14:31:34 +0200 > > > > > > > > From: alexander.h...@mytum.de > > > > > > > > To: gmx-users@gromacs.org > > > > > > > > Subject: [gmx-users] direction_periodic > > > > > > > > > > > > > > > > Hey, > > > > > > > > > > > > > > > > after some pain of merging the dev branch into our 4.0.5 > version > > > > > I got > > > > > > > > the new pull mode "direction_periodic" > > > > > > > > running over the weekend. There's some weird rotation of the > > > pulled > > > > > > > > objects going on and pbc seem weird as well (there are water > > > > > molecules > > > > > > > > in those positions where I'd expect the periodic image of my > > > diamond > > > > > > > > slab which leaves the box at one side). I guess you > tested the > > > > > new pull > > > > > > > > mode somehow, so any ideas what's going on here? I'm still > > > trying to > > > > > > > > perform the same experiment for which I send you the > input files > > > > > while > > > > > > > > ago and for which you kindly implemented the new pull mode. > > > > > > > > > > > > > > > > Thx for your help, > > > > > > > > Alex > > > > > > > > > > > > > > > > Berk Hess schrieb: > > > > > > > > > I have committed a new pull geometry direction_periodic to > > > the git > > > > > > > > > master branch. It is not documented yet. > > > > > > > > > It works the same at direction, but allows distances to be > > > larger > > > > > > > > > than half the box and does not add the pull force to the > > > virial. > > > > > > > > > > > > > > > > > > Berk > > > > > > > > _______________________________________________ > > > > > > > > gmx-users mailing list gmx-users@gromacs.org > > > > > > > > http://lists.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 > > > > > > > > > > > > > > > > > > > > > > > ------------------------------------------------------------------------ > > > > > > > Express yourself instantly with MSN Messenger! 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Read > http://www.gromacs.org/mailing_lists/users.php > > > > > > > > > > > > _______________________________________________ > > > > > > gmx-users mailing list gmx-users@gromacs.org > > > > > > http://lists.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 > > > > > > > > > > > > > > ------------------------------------------------------------------------ > > > > > Express yourself instantly with MSN Messenger! MSN Messenger > > > > > <http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/> > > > > > > > > > ------------------------------------------------------------------------ > > > > > > > > > > _______________________________________________ > > > > > gmx-users mailing list gmx-users@gromacs.org > > > > > http://lists.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 > > > > > > > > _______________________________________________ > > > > gmx-users mailing list gmx-users@gromacs.org > > > > http://lists.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 > > > > > > > ------------------------------------------------------------------------ > > > Express yourself instantly with MSN Messenger! MSN Messenger > > > <http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/> > > > > ------------------------------------------------------------------------ > > > > > > _______________________________________________ > > > gmx-users mailing list gmx-users@gromacs.org > > > http://lists.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 > > > > ------------------------------------------------------------------------ > Express yourself instantly with MSN Messenger! MSN Messenger > <http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/> > ------------------------------------------------------------------------ > > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://lists.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 _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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