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