[gmx-users] direction_periodic

[Berk Hess]

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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