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
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