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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 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 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 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 the git<br>> > > > > > master branch. It is not documented yet.<br>> > > > > > It works the same at direction, but allows distances to be larger<br>> > > > > > than half the box and does not add the pull force to the 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 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>> 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 /><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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