[gmx-users] t_trxframe speed units

[aherz]

sure,

I'll update to the head revision as soon as a fix is available.
Any idea how long this will take?

Alex

Berk Hess schrieb:
> Thinking about this, I will probably not fix it in 4.0,
> but only in git master for 4.1.
>
> There are several issues with pulling "infinitely" long/far.
> One of them is that you can no longer determine the virial contribution.
> Also, grompp should check that you do not pressure coupl in the direction
> that you pull.
>
> Berk
>
> > Date: Fri, 4 Sep 2009 12:45:04 +0200
> > From: alexander.herz at mytum.de
> > To: gmx-users at gromacs.org
> > Subject: Re: [gmx-users] t_trxframe speed units
> >
> > 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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