Hi, thx for suggesting the workaround, just to make sure I understand the workaround correctly:
I devide each slab in 2 sections, one section contains 90% of the atoms (section A), the other the rest (section B). Now I set the pbc_atom to the center atom of section A and pull it using constraints? Alex Berk Hess schrieb: > Hi, > > This is due to the periodicity issue of the COM calculation that I > have mentioned before. > The problem is that some atoms are at close to half a box length from > the pbc_atom > and those can jump back and forth between two periodic images in the > distance calculations. > This "noise" will make the constraint code crash, since it tries to > correct for it immediately. > The umbrella potential smooths this effect out somewhat and can > therefore run stably, > but you would still see the noise in the results. > > Fixing this is difficult, since it would require storing the periodic > image of each atom > in the pull group at the start of the simulation and determining the > image for the COM > calculation using the initial image. Also the checkpoint file should > store the images. > I would not like to put such code in the standard version. > > A workaround could be to pull on 90% of the slabs, leaving a part of > 10% along x out. > Then define the pbc_atom in the middle of the 90%. The 10% will just > move along. > This should solve your problem and should not produce artifacts. > > Berk > > > Date: Fri, 2 Oct 2009 10:25:21 +0200 > > From: alexander.h...@mytum.de > > To: gmx-users@gromacs.org > > Subject: Re: [gmx-users] direction_periodic > > > > You did suggest that, but it crashes at step 0, as said :) > > > > Alex > > > > Berk Hess schrieb: > > > Hi, > > > > > > Then you should use constraint pulling instead of an umbrella > potential. > > > I have been wondering all the time why you are using a potential > > > and not a constraint. I think I had suggested using a constraint some > > > time ago, but I am not sure that I did. > > > > > > Berk > > > > > > > Date: Fri, 2 Oct 2009 09:45:42 +0200 > > > > From: alexander.h...@mytum.de > > > > To: gmx-users@gromacs.org > > > > Subject: Re: [gmx-users] direction_periodic > > > > > > > > Hey, > > > > > > > > I want to pull the diamonds with more or less exactly the speed > I give > > > > for the pulling without the massive noise > > > > (in gromacs 3.3 this worked using afm type pulling, after some > > > > equilibration the slabs settled to an almost constant > > > > pull speed without soo much fluctuation using the same > parameters I use > > > > noew for umbrella). > > > > So I tried using a constraint rather than umbrella, which alwas > crashes > > > > at the first step (even if I did some equilibration > > > > using umbrella pulling beforehands). > > > > > > > > So how can I achieve a pull speed which is about constant 0.01 > nm/ps and > > > > with fluctuations less than 10% of this speed? > > > > > > > > Thx, > > > > Alex > > > > _______________________________________________ > > > > 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 > > > > > > > ------------------------------------------------------------------------ > > > See all the ways you can stay connected to friends and family > > > <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 > > ------------------------------------------------------------------------ > 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
