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