[gmx-users] direction_periodic

[aherz]

Hi,

thx for suggesting the workaround, just to make sure I understand the
workaround correctly:

I devide each slab in 2 sections, one section contains 90% of the atoms
(section A), the other the rest (section B).
Now I set the pbc_atom to the center atom of section A and pull it using
constraints?

Alex

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