[gmx-users] t_trxframe speed units

Berk Hess gmx3 at hotmail.com
Wed Sep 2 16:31:26 CEST 2009 

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