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