[gmx-users] t_trxframe speed units

[aherz]

Hey,

I tried everything you suggested and a couple more things and still it
is not possible to get a reasonable speed
for the pulled groups (always way beyond the 0.01nm/ps set in the mdp
file and mostly containing some high frequence patttern probably related
to pbc). (I tried: constraint, pbcatoms, direction,position and using no
ref group).

Can I send you a small sample system with the problem or is there
something else I can do?

Thx,
Alex

Berk Hess schrieb:
> 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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