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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 the box.<br>But if your force constant is only 1000 it might lag by a lot.<br>Furthermore, if you did not use pull_start, it might start at a random<br>distance with an enormous force.<br><br>Berk<br><br>> Date: Wed, 2 Sep 2009 15:48:56 +0200<br>> From: alexander.herz@mytum.de<br>> To: gmx-users@gromacs.org<br>> Subject: Re: [gmx-users] t_trxframe speed units<br>> <br>> Yes, the diamond moves through the complete sim box (eg. from left to<br>> right) before it pops back to the left side due to pbc.<br>> But looking at the diamond speed (which is increasing) it looks as if<br>> the afm tip is not shifted back to the left side when it leaves the sim<br>> box at the right side. If that was the case then the distance of the tip<br>> and the group would increase all the time<br>> (after the diamond has been shifted back to the left side the first time<br>> due to pbc but the afm is not shifted back) which would explain the<br>> increasing speed of the diamond.<br>> <br>> Let me rephrase the question, what happens with the pull position when<br>> it reaches the box boundaries??<br>> Is it shifted back (so pull_pos[XX]-=box[XX][XX]) or not? Also, are the<br>> atoms shifted back when they leave the box?<br>> <br>> Berk Hess schrieb:<br>> > I don't understand what you want to say.<br>> > The diamond does move a lot right?<br>> ><br>> > I think the main problem might be that you use an umbrella potential<br>> > will an very small force constant (for such large groups).<br>> > Try using pull=constraint.<br>> > (and use pull_start=yes)<br>> ><br>> > Berk<br>> ><br>> > > Date: Wed, 2 Sep 2009 15:22:45 +0200<br>> > > From: alexander.herz@mytum.de<br>> > > To: gmx-users@gromacs.org<br>> > > Subject: Re: [gmx-users] t_trxframe speed units<br>> > ><br>> > > hm..<br>> > ><br>> > > after thinking about this for a sec I'd say I'm missing an option to<br>> > > apply the pbc to the pull position.<br>> > > Currently it looks as if the position of the "afm tip" is moving in<br>> > > absolute coordinates further and further away from the original position<br>> > > while the diamonds stay in the original box due to applied pbc.<br>> > > Therefore the distance of the diamond to the<br>> > > "afm tip" is increasing and hence the force grows bigger and bigger. If<br>> > > I could apply the pbc to the afm position as well then<br>> > > everything would work as expected??<br>> > ><br>> > > Alex<br>> > ><br>> > > Berk Hess schrieb:<br>> > > > Then you were lucky with Gromacs 3.<br>> > > > The pull code in Gromacs 3 does not treat pbc at all,<br>> > > > so I am surprised that it worked.<br>> > > ><br>> > > > I just realized that pull_pbcatom is always set in Gromacs 4.<br>> > > > Maybe it would be enough to add pull_start=yes.<br>> > > ><br>> > > > Berk<br>> > > ><br>> > > > > Date: Wed, 2 Sep 2009 14:38:35 +0200<br>> > > > > From: alexander.herz@mytum.de<br>> > > > > To: gmx-users@gromacs.org<br>> > > > > Subject: Re: [gmx-users] t_trxframe speed units<br>> > > > ><br>> > > > > I will try this, thx for the help.<br>> > > > ><br>> > > > > Anyways, what is the correct way to do what I want with gromacs 4?<br>> > > > > (apparently the setup I tryed to use worked for gromacs 3, since I<br>> > > > > ported the input data<br>> > > > > from old sims and now I'm trying to recreate the old results).<br>> > > > ><br>> > > > > Alex<br>> > > > ><br>> > > > > Berk Hess schrieb:<br>> > > > > > The simple issue is that a center of mass is not uniquely defined<br>> > > > > > for a periodic group of particles.<br>> > > > > > If you work on the velocity level, this problem is easy to solve.<br>> > > > > > But the pull code works on the coordinate level.<br>> > > > > ><br>> > > > > > Try with pull_pbcatom set, it might work.<br>> > > > > ><br>> > > > > > Berk<br>> > > > > ><br>> > > > > ><br>> > > > > >> Date: Wed, 2 Sep 2009 14:11:11 +0200<br>> > > > > >> From: alexander.herz@mytum.de<br>> > > > > >> To: gmx-users@gromacs.org<br>> > > > > >> Subject: Re: [gmx-users] t_trxframe speed units<br>> > > > > >><br>> > > > > >> We wanted to use 2 slabs so that the net impuls is conserved.<br>> > > > > >> Also I'm looking at the slip length, so I actually want to<br>> > > > extract the<br>> > > > > >> velocity profile of the water in between the two diamond<br>> > slabs. I'm<br>> > > > > >> pulling in x (the pull setup is reproduced at the bottom of<br>> > the old<br>> > > > > >> mail) and I'm using pbc in 3d.<br>> > > > > >><br>> > > > > >> What is the problem with pulling the diamond slabs at const<br>> > speed? I<br>> > > > > >> don't actually care where exactly they are.<br>> > > > > >> I only care about the boundary condition at the diamond water<br>> > > > interface<br>> > > > > >> (so that the diamond moves along the surface<br>> > > > > >> with v=cst). I mean, I'm pulling with "direction" not distance,<br>> > > > why does<br>> > > > > >> "direction" care about the COM distance?<br>> > > > > >><br>> > > > > >> Would it work with absolute coords (empty pullgroup0,<br>> > > > pullgroup1=DIAM1<br>> > > > > >> and pullgroup2=DIAM2)??<br>> > > > > >><br>> > > > > >> Alex<br>> > > > > >><br>> > > > > >> Berk Hess schrieb:<br>> > > > > >><br>> > > > > >>> Ah, maybe now I understand the issue.<br>> > > > > >>> Are you pulling in x and are the slabs periodic in x?<br>> > > > > >>> That will not work, as the COM is not defined in a periodic<br>> > > > direction<br>> > > > > >>><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>> > ------------------------------------------------------------------------<br>> > > > Express yourself instantly with MSN Messenger! MSN Messenger<br>> > > > <http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/><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 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>> > > 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>> ><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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