[gmx-users] t_trxframe speed units

[aherz]

Great!

Berk Hess schrieb:
> Ah, now I see what the problem is.
> The pull code works correctly when the distance is shorter or longer
> than half the box length. But when the distance crosses half the box
> length,
> the code might take the "wrong" periodic distance.
> I'll see if I can fix this.
>
> Berk
>
> ------------------------------------------------------------------------
> From: gmx3 at hotmail.com
> To: gmx-users at gromacs.org
> Subject: RE: [gmx-users] t_trxframe speed units
> Date: Fri, 4 Sep 2009 10:25:09 +0200
>
> Hi,
>
> Could you mail me your input files?
>
> Berk
>
> > Date: Fri, 4 Sep 2009 10:05:27 +0200
> > From: alexander.herz at mytum.de
> > To: gmx-users at gromacs.org
> > Subject: Re: [gmx-users] t_trxframe speed units
> >
> > Hi
> >
> > yes, I tried pull_start=yes (you also suggested trying constraint
> > instead of umbrella, which I tried as well).
> > my box is rectangular.
> >
> > Alex
> >
> > Berk Hess schrieb:
> > > Hi,
> > >
> > > The only thing I suggested was using pull_start=yes,
> > > otherwise you will start at a "random" distance and you will have
> enormous forces.
> > > Did you try that?
> > >
> > > Do you have a rectangular or a triclinic box?
> > >
> > > Berk
> > >
> > >
> > >> Date: Thu, 3 Sep 2009 18:00:44 +0200
> > >> From: alexander.herz at mytum.de
> > >> To: gmx-users at gromacs.org
> > >> Subject: Re: [gmx-users] t_trxframe speed units
> > >>
> > >> 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
> > >>>
> > >>>
> ------------------------------------------------------------------------
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