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