[gmx-users] direction_periodic

Thu Oct 1 14:08:28 CEST 2009

Hi,

did you look at the actual trajectory (trr/xtc) or the velocity of one
of the diamond slabs (using g_traj) ?
I do get a sawtooth style COM distance (pullx.xvg) but both the
veloc.xvg and the trajectory show that the slabs are not actually moving
much (the speed of the slab fluctuates wildly around 5e-3nm/ps in a
2500ps run when I'm pulling with 0.01nm/ps).

Alex

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.herz at mytum.de
> > To: gmx-users at 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.herz at mytum.de
> > > > To: gmx-users at 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.herz at mytum.de
> > > > > > To: gmx-users at 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.herz at mytum.de
> > > > > > > > To: gmx-users at 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.herz at mytum.de
> > > > > > > > > > To: gmx-users at 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.herz at mytum.de
> > > > > > > > > > > > To: gmx-users at 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
> > > > > > > > > > > > _______________________________________________
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