[gmx-users] t_trxframe speed units

[Berk Hess]

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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