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Then you were lucky with Gromacs 3.<br>The pull code in Gromacs 3 does not treat pbc at all,<br>so I am surprised that it worked.<br><br>I just realized that pull_pbcatom is always set in Gromacs 4.<br>Maybe it would be enough to add pull_start=yes.<br><br>Berk<br><br>> Date: Wed, 2 Sep 2009 14:38:35 +0200<br>> From: alexander.herz@mytum.de<br>> To: gmx-users@gromacs.org<br>> Subject: Re: [gmx-users] t_trxframe speed units<br>> <br>> I will try this, thx for the help.<br>> <br>> Anyways, what is the correct way to do what I want with gromacs 4?<br>> (apparently the setup I tryed to use worked for gromacs 3, since I<br>> ported the input data<br>> from old sims and now I'm trying to recreate the old results).<br>> <br>> Alex<br>> <br>> Berk Hess schrieb:<br>> > The simple issue is that a center of mass is not uniquely defined<br>> > for a periodic group of particles.<br>> > If you work on the velocity level, this problem is easy to solve.<br>> > But the pull code works on the coordinate level.<br>> ><br>> > Try with pull_pbcatom set, it might work.<br>> ><br>> > Berk<br>> ><br>> > <br>> >> Date: Wed, 2 Sep 2009 14:11:11 +0200<br>> >> From: alexander.herz@mytum.de<br>> >> To: gmx-users@gromacs.org<br>> >> Subject: Re: [gmx-users] t_trxframe speed units<br>> >><br>> >> We wanted to use 2 slabs so that the net impuls is conserved.<br>> >> Also I'm looking at the slip length, so I actually want to extract the<br>> >> velocity profile of the water in between the two diamond slabs. I'm<br>> >> pulling in x (the pull setup is reproduced at the bottom of the old<br>> >> mail) and I'm using pbc in 3d.<br>> >><br>> >> What is the problem with pulling the diamond slabs at const speed? I<br>> >> don't actually care where exactly they are.<br>> >> I only care about the boundary condition at the diamond water interface<br>> >> (so that the diamond moves along the surface<br>> >> with v=cst). I mean, I'm pulling with "direction" not distance, why does<br>> >> "direction" care about the COM distance?<br>> >><br>> >> Would it work with absolute coords (empty pullgroup0, pullgroup1=DIAM1<br>> >> and pullgroup2=DIAM2)??<br>> >><br>> >> Alex<br>> >><br>> >> Berk Hess schrieb:<br>> >> <br>> >>> Ah, maybe now I understand the issue.<br>> >>> Are you pulling in x and are the slabs periodic in x?<br>> >>> That will not work, as the COM is not defined in a periodic direction<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 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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