Hey, could you mail me the complete input files you are using for your test? I'd like to compare them with the stuff I have to see what's wrong.
alexander.h...@mytum.de Thx! Berk Hess schrieb: > Hi, > > I just ran a simulation with your input files. > I only changed the geometry to direction_periodic and increased the > rate to 0.1. > The distance decreases linearly with a slight waviness due to the > harmonic potential. > The location of the reference group shows a sawtooth profile, > as one would expect in a periodic system. > > So it seems to work fine for me. > > Berk > > > Date: Thu, 1 Oct 2009 10:24:54 +0200 > > From: alexander.h...@mytum.de > > To: gmx-users@gromacs.org > > Subject: Re: [gmx-users] direction_periodic > > > > Hey, > > > > did you find the time to look at it? > > > > Thx, > > Alex > > > > Berk Hess schrieb: > > > I am not sure I continued the simulation long enough. > > > I'll run it again tomorrow. > > > > > > Berk > > > > > > > Date: Mon, 28 Sep 2009 16:57:19 +0200 > > > > From: alexander.h...@mytum.de > > > > To: gmx-users@gromacs.org > > > > Subject: Re: [gmx-users] direction_periodic > > > > > > > > Well..they do move forward for a few ps and then they move back > (they > > > > oscillate). > > > > Did you check for a longer period? > > > > > > > > Alex > > > > > > > > Berk Hess schrieb: > > > > > Strange... > > > > > I tested the code on the files you sent me > > > > > and the slabs were moving smoothly. > > > > > > > > > > Berk > > > > > > > > > > > Date: Mon, 28 Sep 2009 15:40:16 +0200 > > > > > > From: alexander.h...@mytum.de > > > > > > To: gmx-users@gromacs.org > > > > > > Subject: Re: [gmx-users] direction_periodic > > > > > > > > > > > > Hey, > > > > > > > > > > > > so using the new direction_periodic with some kernels that > > > actually work > > > > > > and the sources from the git (unmodified) > > > > > > gives a nice smooth pull force but no actual mean displacement > > > of the > > > > > > groups to be pulled (on average they just stay where they > are,see > > > > > > attached graph). I'm still trying to pull them into opposite > > > directions > > > > > > though. > > > > > > > > > > > > I'm using this setup: > > > > > > pull = umbrella > > > > > > pull_geometry = direction_periodic > > > > > > pull_ngroups = 1 > > > > > > pull_group0 = DIAM > > > > > > pull_group1 = DIAM2 > > > > > > pulldim = Y N N > > > > > > pull_k1 = 1000.0 > > > > > > pull_rate1 = 0.01 > > > > > > pull_vec1 = -1.0 0.0 0.0 > > > > > > > > > > > > How can I make the two diamond slabs actually move in opposite > > > > > > directions rather than just oscillating around their > > > > > > initial positions? > > > > > > > > > > > > Thx, > > > > > > Alex > > > > > > > > > > > > Berk Hess schrieb: > > > > > > > Hi, > > > > > > > > > > > > > > Don't use fortran. > > > > > > > We will get rid of it before the 4.1 release. > > > > > > > > > > > > > > Berk > > > > > > > > > > > > > > > Date: Mon, 21 Sep 2009 16:17:17 +0200 > > > > > > > > From: alexander.h...@mytum.de > > > > > > > > To: gmx-users@gromacs.org > > > > > > > > Subject: Re: [gmx-users] direction_periodic > > > > > > > > > > > > > > > > Hey, > > > > > > > > > > > > > > > > ok, I checked this. It works ok with the assembly > kernels on my > > > > > local > > > > > > > > machine, but it fails with fortran kernels > > > > > > > > on the HPC and on my local machine. > > > > > > > > > > > > > > > > Alex > > > > > > > > > > > > > > > > Berk Hess schrieb: > > > > > > > > > Yes. > > > > > > > > > > > > > > > > > > Berk > > > > > > > > > > > > > > > > > > > Date: Mon, 21 Sep 2009 14:42:43 +0200 > > > > > > > > > > From: alexander.h...@mytum.de > > > > > > > > > > To: gmx-users@gromacs.org > > > > > > > > > > Subject: Re: [gmx-users] direction_periodic > > > > > > > > > > > > > > > > > > > > With master branch you mean the code I get via > > > > > > > > > > > > > > > > > > > > |git clone git://git.gromacs.org/gromacs.git > > > > > > > > > > > > > > > > > > > > right? > > > > > > > > > > > > > > > > > > > > Alex > > > > > > > > > > | > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > Berk Hess schrieb: > > > > > > > > > > > I tested on your system and got good results. > > > > > > > > > > > There is still a tricky issue: the pull COM is still > > > > > determined > > > > > > > > > > > in the "standard" way by summing distances from the > > > pbcatom. > > > > > > > > > > > Therefore atoms should not change nearest image > from he > > > > > pbcatom. > > > > > > > > > > > This would result in nasty noise in the pull COM and > > > force. > > > > > > > > > > > > > > > > > > > > > > I would suggest that you try to run the master > branch and > > > > > check > > > > > > > > > > > if that works. > > > > > > > > > > > > > > > > > > > > > > Berk > > > > > > > > > > > > > > > > > > > > > > > Date: Mon, 21 Sep 2009 14:31:34 +0200 > > > > > > > > > > > > From: alexander.h...@mytum.de > > > > > > > > > > > > To: gmx-users@gromacs.org > > > > > > > > > > > > Subject: [gmx-users] direction_periodic > > > > > > > > > > > > > > > > > > > > > > > > Hey, > > > > > > > > > > > > > > > > > > > > > > > > after some pain of merging the dev branch into > our 4.0.5 > > > > > version > > > > > > > > > I got > > > > > > > > > > > > the new pull mode "direction_periodic" > > > > > > > > > > > > running over the weekend. There's some weird > > > rotation of the > > > > > > > pulled > > > > > > > > > > > > objects going on and pbc seem weird as well (there > > > are water > > > > > > > > > molecules > > > > > > > > > > > > in those positions where I'd expect the periodic > > > image of my > > > > > > > diamond > > > > > > > > > > > > slab which leaves the box at one side). I guess you > > > > > tested the > > > > > > > > > new pull > > > > > > > > > > > > mode somehow, so any ideas what's going on here? I'm > > > still > > > > > > > trying to > > > > > > > > > > > > perform the same experiment for which I send you the > > > > > input files > > > > > > > > > while > > > > > > > > > > > > ago and for which you kindly implemented the new > > > pull mode. > > > > > > > > > > > > > > > > > > > > > > > > Thx for your help, > > > > > > > > > > > > Alex > > > > > > > > > > > > > > > > > > > > > > > > Berk Hess schrieb: > > > > > > > > > > > > > I have committed a new pull geometry > > > direction_periodic to > > > > > > > the git > > > > > > > > > > > > > master branch. It is not documented yet. > > > > > > > > > > > > > It works the same at direction, but allows > > > distances to be > > > > > > > larger > > > > > > > > > > > > > than half the box and does not add the pull force > > > to the > > > > > > > virial. > > > > > > > > > > > > > > > > > > > > > > > > > > Berk > > > > > > > > > > > > _______________________________________________ > > > > > > > > > > > > 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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