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Thinking about this, I will probably not fix it in 4.0,<br>but only in git master for 4.1.<br><br>There are several issues with pulling "infinitely" long/far.<br>One of them is that you can no longer determine the virial contribution.<br>Also, grompp should check that you do not pressure coupl in the direction<br>that you pull.<br><br>Berk<br><br>> Date: Fri, 4 Sep 2009 12:45:04 +0200<br>> From: alexander.herz@mytum.de<br>> To: gmx-users@gromacs.org<br>> Subject: Re: [gmx-users] t_trxframe speed units<br>> <br>> Great!<br>> <br>> Berk Hess schrieb:<br>> > Ah, now I see what the problem is.<br>> > The pull code works correctly when the distance is shorter or longer<br>> > than half the box length. But when the distance crosses half the box<br>> > length,<br>> > the code might take the "wrong" periodic distance.<br>> > I'll see if I can fix this.<br>> ><br>> > Berk<br>> ><br>> > ------------------------------------------------------------------------<br>> > From: gmx3@hotmail.com<br>> > To: gmx-users@gromacs.org<br>> > Subject: RE: [gmx-users] t_trxframe speed units<br>> > Date: Fri, 4 Sep 2009 10:25:09 +0200<br>> ><br>> > Hi,<br>> ><br>> > Could you mail me your input files?<br>> ><br>> > Berk<br>> ><br>> > > Date: Fri, 4 Sep 2009 10:05:27 +0200<br>> > > From: alexander.herz@mytum.de<br>> > > To: gmx-users@gromacs.org<br>> > > Subject: Re: [gmx-users] t_trxframe speed units<br>> > ><br>> > > Hi<br>> > ><br>> > > yes, I tried pull_start=yes (you also suggested trying constraint<br>> > > instead of umbrella, which I tried as well).<br>> > > my box is rectangular.<br>> > ><br>> > > Alex<br>> > ><br>> > > Berk Hess schrieb:<br>> > > > Hi,<br>> > > ><br>> > > > The only thing I suggested was using pull_start=yes,<br>> > > > otherwise you will start at a "random" distance and you will have<br>> > enormous forces.<br>> > > > Did you try that?<br>> > > ><br>> > > > Do you have a rectangular or a triclinic box?<br>> > > ><br>> > > > Berk<br>> > > ><br>> > > ><br>> > > >> Date: Thu, 3 Sep 2009 18:00:44 +0200<br>> > > >> From: alexander.herz@mytum.de<br>> > > >> To: gmx-users@gromacs.org<br>> > > >> Subject: Re: [gmx-users] t_trxframe speed units<br>> > > >><br>> > > >> Hey,<br>> > > >><br>> > > >> I tried everything you suggested and a couple more things and<br>> > still it<br>> > > >> is not possible to get a reasonable speed<br>> > > >> for the pulled groups (always way beyond the 0.01nm/ps set in the mdp<br>> > > >> file and mostly containing some high frequence patttern probably<br>> > related<br>> > > >> to pbc). (I tried: constraint, pbcatoms, direction,position and<br>> > using no<br>> > > >> ref group).<br>> > > >><br>> > > >> Can I send you a small sample system with the problem or is there<br>> > > >> something else I can do?<br>> > > >><br>> > > >> Thx,<br>> > > >> Alex<br>> > > >><br>> > > >> Berk Hess schrieb:<br>> > > >><br>> > > >>> But you can not talk about popping back, since there is pbc.<br>> > > >>> What matters is how the pull code determines the distance.<br>> > > >>> At least in 4.0.4 and 4.0.5 it add the rate*t before doing pbc,<br>> > > >>> such that it pulls smoothly even if the distance is larger than<br>> > the box<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<br>> > 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<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>> > What can you do with the new Windows Live? Find out<br>> > <http://www.microsoft.com/windows/windowslive/default.aspx><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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